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Table of Contents 
Endicott Biofuel Production Facility Project November 2013 
Initial Study ii 
3.5.7. Production Tanks (Biofuels Production Facility) and Storage Tanks (Targa 
Terminal) ............................................................................................................. 3-32 
3.5.8. Nitrogen Production ................................................................................. 3-33 
3.5.9. Thermal Oxidizer ..................................................................................... 3-33 
3.5.10. Fire Protection ....................................................................................... 3-33 
3.5.11. Lighting ................................................................................................. 3-34 
3.5.12. Security ................................................................................................. 3-34 
3.5.13. Access and Product Off-site Transport .................................................. 3-35 
3.5.14. Emergency Shut Down System ............................................................. 3-35 
3.5.15. Cathodic Protection ............................................................................... 3-35 
3.5.16. Pipeline Supply Connections ................................................................. 3-35 
3.5.17. Stormwater Runoff Plan ........................................................................ 3-37 
3.6 BIOFUEL PRODUCTION FACILITY CONSTRUCTION ................................... 3-37 
3.6.1. Project Construction ................................................................................ 3-37 
3.6.2. Pipeline Construction .............................................................................. 3-39 
3.6.3. Project Schedule, Workforce, and Construction Hours ............................ 3-41 
3.6.4. Construction Traffic ................................................................................. 3-41 
3.7 BIOFUEL PRODUCTION FACILITY OPERATIONS ........................................ 3-43 
3.7.1. Employment, Operating Hours, and Anticipated Traffic ........................... 3-43 
3.8 SUMMARY OF MITIGATION MEASURES ...................................................... 3-44 
3.8.1. Aesthetics (Visual Resources) ................................................................. 3-44 
3.8.2. Agriculture and Forestry Resources ........................................................ 3-44 
3.8.3. Air Quality................................................................................................ 3-44 
3.8.4. Biological Resources ............................................................................... 3-45 
3.8.5. Cultural Resources .................................................................................. 3-45 
3.8.6. Geology and Soils ................................................................................... 3-46 
3.8.7. Greenhouse Gas Emissions .................................................................... 3-46 
3.8.8. Hazards and Hazardous Materials .......................................................... 3-46 
3.8.9. Hydrology and Water Quality ................................................................... 3-46 
3.8.10. Land Use and Planning ......................................................................... 3-47 
3.8.11. Mineral Resources ................................................................................ 3-47 
3.8.12. Noise ..................................................................................................... 3-47 
3.8.13. Population and Housing ........................................................................ 3-48 
3.8.14. Public Services ...................................................................................... 3-48 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study iii 
3.8.15. Recreation ............................................................................................. 3-48 
3.8.16. Transportation/Traffic ............................................................................ 3-48 
3.8.17. Utilities and Service Systems ................................................................ 3-48 
4.0 ENVIRONMENTAL FACTORS POTENTIALLY AFFECTED ........................................ 4-1 
5.0 DETERMINATION ......................................................................................................... 5-1 
6.0 DISCUSSION OF ENVIRONMENTAL SETTING, POTENTIAL IMPACTS, AND 
MITIGATION MEASURES ............................................................................................ 6-1 
6.1 AESTHETICS (VISUAL RESOURCES) ............................................................. 6-3 
6.1.1. Background ............................................................................................... 6-3 
6.1.2. Methodology .............................................................................................. 6-5 
6.1.3. Environmental Setting ............................................................................... 6-7 
6.1.4. Standards of Significance ........................................................................ 6-13 
6.1.5. Impacts and Mitigation Measures ............................................................ 6-13 
6.1.6. Aesthetics Initial Study Responses .......................................................... 6-13 
6.1.7. Responses to Initial Study Questions ...................................................... 6-14 
6.2 AGRICULTURE AND FORESTRY RESOURCES ........................................... 6-15 
6.2.1. Background ............................................................................................. 6-15 
6.2.2. Methodology ............................................................................................ 6-15 
6.2.3. Environmental Setting ............................................................................. 6-15 
6.2.4. Standards of Significance ........................................................................ 6-16 
6.2.5. Impacts and Mitigation Measures ............................................................ 6-16 
6.2.6. Agriculture and Forestry Initial Study Responses .................................... 6-17 
6.2.7. Responses to Initial Study Questions ...................................................... 6-18 
6.3 AIR QUALITY .................................................................................................. 6-19 
6.3.1. Background ............................................................................................. 6-19 
6.3.2. Methodology ............................................................................................ 6-29 
6.3.3. Environmental Setting ............................................................................. 6-30 
6.3.4. Standards of Significance ........................................................................ 6-33 
6.3.5. Impacts and Mitigation Measures ............................................................ 6-35 
6.3.6. Air Quality Initial Study Responses .......................................................... 6-43 
6.3.7. Responses to Initial Study Questions ...................................................... 6-43 
6.4 BIOLOGICAL RESOURCES ............................................................................ 6-46 
6.4.1. Background ............................................................................................. 6-46 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study iv 
6.4.2. Methodology ............................................................................................ 6-50 
6.4.3. Environmental Setting ............................................................................. 6-50 
6.4.4. Standards of Significance ........................................................................ 6-64 
6.4.5. Impacts and Mitigation Measures ............................................................ 6-66 
6.4.6. Biological Resources Initial Study Responses ......................................... 6-67 
6.4.7. Responses to Initial Study Questions ...................................................... 6-68 
6.5 CULTURAL RESOURCES .............................................................................. 6-69 
6.5.1. Background ............................................................................................. 6-69 
6.5.2. Methodology ............................................................................................ 6-74 
6.5.3. Environmental Setting ............................................................................. 6-74 
6.5.4. Standards of Significance ........................................................................ 6-76 
6.5.5. Impacts and Mitigation Measures ............................................................ 6-77 
6.5.6. Cultural Resources Initial Study Responses ............................................ 6-78 
6.5.7. Response to Questions ........................................................................... 6-78 
6.6 GEOLOGY, SOILS, AND SEISMICITY ............................................................ 6-80 
6.6.1. Background ............................................................................................. 6-80 
6.6.2. Methodology ............................................................................................ 6-80 
6.6.3. Environmental Setting ............................................................................. 6-80 
6.6.4. Standards of Significance ........................................................................ 6-84 
6.6.5. Impacts and Mitigation Measures ............................................................ 6-85 
6.6.6. Geology, Soils, and Seismicity Initial Study Responses........................... 6-86 
6.6.7. Responses to Initial Study Questions ...................................................... 6-87 
6.7 GREEN HOUSE GAS EMISSIONS ................................................................. 6-90 
6.7.1. Background ............................................................................................. 6-90 
6.7.2. Methodology ............................................................................................ 6-92 
6.7.3. Environmental Setting ............................................................................. 6-92 
6.7.4. Standards of Significance ........................................................................ 6-92 
6.7.5. Impacts and Mitigation Measures ............................................................ 6-92 
6.7.6. Green House Gas Initial Study Responses.............................................. 6-93 
6.7.7. Response to Initial Study Questions ........................................................ 6-93 
6.8 HAZARDS AND HAZARDOUS MATERIALS ................................................... 6-94 
6.8.1. Background ............................................................................................. 6-94 
6.8.2. Methodology .......................................................................................... 6-100 
6.8.3. Environmental Setting ........................................................................... 6-100 

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Initial Study v 
6.8.4. Standards of Significance ...................................................................... 6-104 
6.8.5. Impacts and Mitigation Measures .......................................................... 6-105 
6.8.6. Hazards and Hazardous Materials Initial Study Responses ................... 6-110 
6.8.7. Responses to Initial Study Questions .................................................... 6-111 
6.9 HYDROLOGY AND WATER QUALITY .......................................................... 6-114 
6.9.1. Background ........................................................................................... 6-114 
6.9.2. Methodology .......................................................................................... 6-117 
6.9.3. Environmental Setting ........................................................................... 6-117 
6.9.4. Standards of Significance ...................................................................... 6-122 
6.9.5. Impacts and Mitigation Measures .......................................................... 6-122 
6.9.6. Hydrology and Water Quality Initial Study Responses ........................... 6-127 
6.9.7. Responses to Initial Study Questions .................................................... 6-128 
6.10 LAND USE AND PLANNING ...................................................................... 6-131 
6.10.1. Background ......................................................................................... 6-131 
6.10.2. Methodology ........................................................................................ 6-133 
6.10.3. Environmental Setting ......................................................................... 6-133 
6.10.4. Standards of Significance .................................................................... 6-137 
6.10.5. Impacts and Mitigation Measures ........................................................ 6-137 
6.10.6. Land Use and Planning Initial Study Responses ................................. 6-138 
6.10.7. Response to Questions ....................................................................... 6-138 
6.11 MINERAL RESOURCES ............................................................................ 6-140 
6.11.1. Background ......................................................................................... 6-140 
6.11.2. Methodology ........................................................................................ 6-141 
6.11.3. Environmental Setting ......................................................................... 6-141 
6.11.4. Standards of Significance .................................................................... 6-141 
6.11.5. Impacts and Mitigation Measures ........................................................ 6-141 
6.11.6. Mineral Resources Initial Study Responses ......................................... 6-142 
6.11.7. Responses to Initial Study Questions .................................................. 6-142 
6.12 NOISE ........................................................................................................ 6-143 
6.12.1. Background ......................................................................................... 6-143 
6.12.2. Methodology ........................................................................................ 6-152 
6.12.3. Environmental Setting ......................................................................... 6-155 
6.12.4. Standards of Significance .................................................................... 6-155 
6.12.5. Impacts and Mitigation Measures ........................................................ 6-156 

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Initial Study vi 
6.12.6. Noise Initial Study Responses ............................................................. 6-160 
6.12.7. Response to Initial Study Questions .................................................... 6-160 
6.13 POPULATION AND HOUSING .................................................................. 6-163 
6.13.1. Background ......................................................................................... 6-163 
6.13.2. Methodology ........................................................................................ 6-163 
6.13.3. Standards of Significance .................................................................... 6-163 
6.13.4. Environmental Setting ......................................................................... 6-164 
6.13.5. Impacts and Mitigation Measures ........................................................ 6-164 
6.13.6. Population and Housing Initial Study Responses ................................. 6-165 
6.13.7. Responses to Initial Study Questions .................................................. 6-165 
6.14 PUBLIC SERVICES AND FACILITIES ....................................................... 6-166 
6.14.1. Background ......................................................................................... 6-166 
6.14.2. Methodology ........................................................................................ 6-170 
6.14.3. Environmental Setting ......................................................................... 6-170 
6.14.4. Standards of Significance .................................................................... 6-175 
6.14.5. Impacts and Mitigation Measures ........................................................ 6-175 
6.14.6. Public Services and Facilities Initial Study Responses ........................ 6-176 
6.14.7. Response to Questions ....................................................................... 6-176 
6.15 RECREATION ............................................................................................ 6-178 
6.15.1. Background ......................................................................................... 6-178 
6.15.2. Methodology ........................................................................................ 6-178 
6.15.3. Environmental Setting ......................................................................... 6-178 
6.15.4. Standards of Significance .................................................................... 6-179 
6.15.5. Impacts and Mitigation Measures ........................................................ 6-179 
6.15.6. Recreation Initial Study Responses ..................................................... 6-181 
6.15.7. Responses to Initial Study Questions .................................................. 6-181 
6.16 TRANSPORTATION/TRAFFIC .................................................................. 6-182 
6.16.1. Background ......................................................................................... 6-182 
6.16.2. Methodology ........................................................................................ 6-185 
6.16.3. Environmental Setting ......................................................................... 6-192 
6.16.4. Standards of Significance .................................................................... 6-193 
6.16.5. Impacts and Mitigation Measures ........................................................ 6-194 
6.16.6. Transportation/Traffic Initial Study Responses .................................... 6-199 
6.16.7. Responses to Initial Study Questions .................................................. 6-200 

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Initial Study vii 
6.17 UTILITIES AND SERVICE SYSTEMS ........................................................ 6-204 
6.17.1. Background ......................................................................................... 6-204 
6.17.2. Methodology ........................................................................................ 6-205 
6.17.3. Environmental Setting ......................................................................... 6-206 
6.17.4. Standards of Significance .................................................................... 6-211 
6.17.5. Impacts and Mitigation Measures ........................................................ 6-211 
6.17.6. Utilities and Service System Responses.............................................. 6-215 
6.17.7. Responses to Initial Study Questions .................................................. 6-216 
6.18 MANDATORY FINDINGS OF SIGNIFICANCE .......................................... 6-219 
6.18.1. Responses to Initial Study Questions .................................................. 6-219 
7.0 FISH AND GAME DETERMINATION ............................................................................ 7-1 
7.1 FISH AND GAME DETERMINATION ................................................................ 7-1 
8.0 REFERENCES .............................................................................................................. 8-1 
8.1 PRINTED REFERENCES AND WEBSITES ...................................................... 8-1 
8.2 INTERVIEWS AND PHONE CONTACTS .......................................................... 8-9 
9.0 AGENCIES AND PERSONS CONTACTED .................................................................. 9-1 
10.0 REPORT PREPARERS ............................................................................................... 10-1 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study viii 
LIST OF FIGURES 
Figure 1.0-1: Vicinity and Location Map ....................................................................... 1-3 
Figure 1.0-2: Biofuel Facility, Pipelines, Truck Rack, Rail Rack, Berth #9 and Storage 
Facilities Map ............................................................................................................... 1-4 
Figure 3.2-1: Endicott Biofuel Production Facility Site Plan .......................................... 3-2 
Figure 3.4-1: Regional Location Map ......................................................................... 3-11 
Figure 3.4-2: AssessorÕs Map ..................................................................................... 3-12 
Figure 3.4-3: Project Setting ....................................................................................... 3-14 
Figure 3.5-1: Biofuel Production Facility (ISBL) .......................................................... 3-16 
Figure 3.5-2 Berth Layout Plan .................................................................................. 3-24 
Figure 3.5-3 Pipeline Route and Connection Map ...................................................... 3-25 
Figure 3.5-4 Targa Terminal Site Plan for Endicott Storage and Transfer Improvements 
.................................................................................................................................. 3-30 
Figure 3.6-1 Staging & Storage Area During Construction ......................................... 3-42 
Figure 6.1-1: Proposed Site Elevation Plan ................................................................ 6-11 
Figure 6.1-2: Endicott Project KOPs Views ................................................................ 6-12 
Figure 6.3-1: California Air Basin Map ........................................................................ 6-21 
Figure 6.4-1: California Natural Diversity Data Base Map .......................................... 6-53 
Figure 6.5-1: Area of Potential Effect / Cultural-Archaeological ................................. 6-70 
Figure 6.6-1: Soil Survey ............................................................................................ 6-82 
Figure 6.6-2: Fault Map .............................................................................................. 6-83 
Figure 6.10-1: General Plan Map ............................................................................. 6-135 
Figure 6.10-2: Zoning Map ....................................................................................... 6-136 
Figure 6.15-1: Neighborhood Parks & Recreation Areas Map ................................. 6-180 
Figure 6.16-1: Traffic Study Intersections ................................................................. 6-187 
Figure 6.16-2: Vehicle Queuing Limits Ð Current Configuration ............................... 6-196 
Figure 6.16-3: Vehicle Queuing Limits Ð Realigned Navy Drive, with Dedicated Right 
Turn Lanes on Navy Drive and Washington Street Year 2030 ................................. 6-197 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study ix 
LIST OF TABLES 
Table 3.3-1: Potentially Applicable Compliance and Review Requirements ................ 3-3 
Table 3.4-1: Biofuel Production Facility Input/Output Volumes .................................... 3-6 
Table 3.5-1: Unit 1 Consumption ................................................................................ 3-17 
Table 3.5-2 Unit 2 Consumption ................................................................................. 3-18 
Table 3.5-3: Unit 3 Consumption ................................................................................ 3-19 
Table 3.5-4: Unit 4 Consumption ................................................................................ 3-20 
Table 3.5-5: Unit 5 Consumption ................................................................................ 3-21 
Table 3.5-6: Unit 6 Consumption ................................................................................ 3-22 
Table 3.5-7: Barge Traffic ........................................................................................... 3-23 
Table 3.5-8: Estimated Truck Traffic .......................................................................... 3-28 
Table 3.5-9: Proposed Rail Demand .......................................................................... 3-31 
Table 3.5-10: Pipelines ............................................................................................... 3-36 
Table 6.1-1: Viewshed Ratings .................................................................................... 6-6 
Table 6.1-1: Aesthetics Initial Study Responses ........................................................ 6-13 
Table 6.2-1: Agriculture and Forestry Initial Study Responses ................................... 6-17 
Table 6.3-1: National Ambient Air Quality Standards ................................................. 6-20 
Table 6.3-2: California Ambient Air Quality Standards ............................................... 6-23 
Table 6.3-3: Ambient Air Monitoring Sites near the Proposed Endicott project .......... 6-25 
Table 6.3-4: Major Source Emission Thresholds ........................................................ 6-25 
Table 6.3-5: Emission Offset Threshold Levels .......................................................... 6-26 
Table 6.3-6: SJVAPCD Control District Thresholds of Significance ........................... 6-28 
Table 6.3-7: Traditional Biodiesel Methanol Emissions .............................................. 6-29 
Table 6.3-8: General Construction Assumptions ........................................................ 6-35 
Table 6.3-9: Phase-specific Construction Assumptions ............................................. 6-36 
Table 6.3-10: Construction Emissions Estimates ....................................................... 6-37 
Table 6.3-11: Boiler Emissions Estimates .................................................................. 6-38 
Table 6.3-12: Production Tanks ................................................................................. 6-38 
Table 6.3-13: Methanol Tank Emissions .................................................................... 6-39 
Table 6.3-14: Vehicle Traffic Assumptions ................................................................. 6-39 
Table 6.3-15: Operational Employee Traffic Emissions Estimates ............................. 6-40 
Table 6.3-16: Total Operational Emissions ................................................................ 6-40 
Table 6.3-17: Air Quality Initial Study Responses ...................................................... 6-43 
Table 6.4-1: Special-status Species Potentially Occurring on the Proposed Lease Area 
.................................................................................................................................. 6-54 
Table 6.4-2: Biological Resources Initial Study Responses ....................................... 6-67 
Table 3.5-1: Cultural Resources Initial Study Responses .......................................... 6-78 
Table 6.6-1: Geology, Soils, and Seismicity Initial Study Responses ......................... 6-86 
Table 3.7-1 Green House Gas Initial Study Responses ............................................. 6-93 
Table 6.8-1: 2013 Environmental Database Report Findings ................................... 6-101 
Table 6.8-2: Hazardous Waste Initial Study Responses .......................................... 6-110 
Table 6.9-1: Hydrology and Water Quality Initial Study Responses ......................... 6-127 
Table 6.10-1: Applicable Land Use Policies ............................................................. 6-133 
Table 6.10-2: Land Use and Planning Initial Study Responses ................................ 6-138 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study x 
Table 6.11-1: Mineral Resources Initial Study Responses ....................................... 6-142 
Table 6.12-1: Definitions of Acoustical Terms .......................................................... 6-149 
Table 6.12-2: Typical Sound Levels Measured in the Environment ......................... 6-151 
Table 6.12-3. Stockton Maximum Allowable Ambient Noise Exposure by Land Use6-154 
Table 6.12-4: Estimated Noise Levels ...................................................................... 6-157 
Table 6.12-5: Noise Initial Study Responses ............................................................ 6-160 
Table 6.13-1: Population and Housing Initial Study Responses ............................... 6-165 
Table 6.14-1: Public Services and Facilities Initial Study Responses ...................... 6-176 
Table 6.15-1: Recreation Initial Study Responses ................................................... 6-181 
Table 6.16-1: Laws, Ordinances, Regulations, and Standards (LORS) ................... 6-183 
Table 6.16-2: Intersection Level of Service (LOS) Definitions .................................. 6-189 
Table 6.16-3: Total Traffic Volumes and LOS .......................................................... 6-191 
Table 6.16-4. Trip Generation Summary Ð Construction Phase. ............................. 6-194 
................................................................................................................................ 6-197 
Table 6.16-5: Transportation/Traffic Initial Study Responses ................................... 6-199 
Table 6.17-1 Ð Electrical Load Summary ................................................................. 6-210 
Table 6.17-3: Utilities and Services Initial Study Responses .................................... 6-215 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study xi 
LIST OF ATTACHMENTS 
Appendix A Ð Proposed Mitigated Negative Declaration 
Appendix B Ð Mitigation Monitoring and Reporting Plan 
Appendix C Ð Lease Legal Description and Alta Survey 
Appendix D Ð Cultural Resources Documentation 
Appendix E Ð Air Quality Modeling Technical Information 
Appendix F Ð Phase I Environmental Assessment 
Appendix G Ð Geotechnical Report 
Appendix H Ð Engineering Feasibility Report 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study xii 
LIST OF ACRONYMS 
ABÑ Assembly Bill 
AB 32ÑCaliforniaÕs Global Warming Solutions Act, Assembly Bill 32 
AC PavingÑAsphalt Concrete 
ADTÑ Average Daily Traffic 
AIChEÑ American Institute of Chemical Engineers 
ALTAÑAmerican Land Title Association 
ANSIÑAmerican National Standards Institute 
APCDÑAir Pollution Control District 
APIÑAmerican Petroleum Institute 
API StandardsÑ American Petroleum Institute Standards for Petroleum Storage Tanks 
APNÑAssessorÕs Parcel Number 
ASMEÑAmerican Society of Mechanical Engineering 
ASTÑAboveground Storage Tank 
ASTMÑAmerican Society for Testing and Materials 
B100ÑPure Fatty Acid Methyl Esters 
BACTÑBest Available Emission Control Technology 
BBLÑ42 gallons per barrel 
BMPÑ Best Management Practices 
BODÑBiochemical Oxygen Demand 
BPÑBefore Present 
BPDÑBarrels Per Day 
BPSÑ Best Performance Standards 
BPHÑBarrels Per Hour 
CAAÑClean Air Act 
CAAQSÑ California Ambient Air Quality Standards 
CalEEModÑCalifornia Emissions Estimator Model 
Cal/EPAÑ California Environmental Protection Agency 
Cal/OSHAÑCalifornia Occupational Safety and Health Agency 
CalRecycleÑ Department of Resources Recycling and Recovery 
CaltransÑ California Department of Transportation 
CWSCÑ California Water Service Company 
CARBÑ California Air Resources Board 
CBCÑCalifornia Building Code 
CCAAÑ California Clean Air Act 
CCAPÑ Climate Change Action Plan 
CCPSÑCenter for Chemical Process Safety 
CCRÑCalifornia Code of Regulations 
CDÑCommunity Design 
CDFFPÑCalifornia Department of Forestry and Fire Protection 
CDFWÑCalifornia Department of Fish and Wildlife 
CECÑCalifornia Energy Commission 
CERCLAÑ Comprehensive Environmental Response Compensation and Liability Act 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study xiii 
CERCLIS-NFPRAÑ U.S. EPA Comprehensive Environmental Response, Compensation, and 
Liability Information System - No Further Remediation Action Planned List 
CEQAÑ California Environmental Quality Act 
CESAÑ California Endangered Species Act 
CFGÑ California Fish and Game Code 
CFMÑCubic Feet per Minute 
CFPÑCalifornia Fully Protected (species) 
CFRÑCode of Federal Regulations 
CHÑ Critical habitat 
CHMIRSÑ Chemical Hazardous Materials Incident Report System 
CHSCÑ California Health and Safety Code 
CityÑCity of Stockton 
CIWMBÑ California Integrated Waste Management Board 
CLSMÑControlled Low-Strength Material 
CNDDBÑ California Natural Diversity Data Base 
CNELÑ Community Noise Equivalent Level 
CNPSÑ California Native Plant Society 
COÑCarbon Monoxide 
CO2ÑCarbon Dioxide 
CO2eÑEquivalent Carbon Dioxide 
CODÑChemical Oxygen Demand 
CorpsÑ United States Army Corps of Engineers 
CORRACTS listÑResources Conservation and Recovery Act Corrective Action List 
CountyÑSan Joaquin County 
CSCÑ California species of concern 
CSFMÑ California State Fire Marshal 
CSLCÑ California State Lands Commission 
CSUSÑ California State University System 
CTRÑ California Toxics Regulations 
CUPAÑ Certified Unified Program Agency 
CWAÑCalifornia Waterfowl Association 
dBÑDecibel 
dBAÑA-Weighted Decibel 
DCMAÑDouble-Counter-Weighted Marine Arms 
DDTÑDichlorodiphenyltrichloroethane 
DeltaÑ Sacramento -San Joaqu’n River Delta 
DFWÑCalifornia Department of Fish and Wildlife 
DHSÑ Department of Homeland Security 
DOÑ Dissolved Oxygen 
DODÑDepartment of Defense 
DOIÑ Department of the Interior 
DOTÑ United States Department of Transportation 
DSPÑDevelopment Standards Plan 
DTSCÑ Department of Toxic Substances Control 
DWSCÑDeep Water Shipping Channel 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study xiv 
EBFÑEndicott Biofuels 
EMDÑEmergency Medical Dispatch 
EMSÑEmergency Medical Services 
EMTÑEmergency Medical Technician 
ENÑEuropean Standardization 
EPCRAÑEmergency Planning & Community Right to Know Act 
EDRÑ Environmental Data Resources 
EEZÑ Exclusive Economic Zone 
EIRÑEnvironmental Impact Report 
EPAÑUnited States Environmental Protection Agency 
ESAÑEnvironmental Site Assessment 
ERNSÑ United States Environmental Protection Agency Emergency Response Notification 
System 
FAAÑFederal Aviation Administration 
FAME Ñ Fatty Acid Methyl Esters 
FARÑ Floor Area Ratio 
FEÑ Federally endangered 
Fed/ OSHAÑ Occupational Safety Health Administration 
FeCl3ÑFerric Chloride 
FEMAÑ Federal Emergency Management Agency 
FESAÑ Federal Endangered Species Act 
FFAÑFree Fatty Acid 
FIRMÑ Flood Insurance Rate Map 
FMMPÑ Farmland Mapping and Monitoring Program 
FOGÑFats, Oils, and Grease 
FRAÑ Federal Railroad Administration 
FSAÑ Facility Security Assessment 
FSOÑ Facility Security Officer 
FSPÑ Facility Security Plan 
FTÑ Federally threatened 
FTAÑFederal Transit Administration 
GAMAQIÑ Guide for Assessing and Mitigating Air Quality Impacts 
GHGÑGreenhouse Gas Emissions 
GIPÑ General Industrial Permit 
GPDÑGallons Per Day 
GPMÑGallons Per Minute 
Great ValleyÑ Great Valley geomorphic province 
HAPÑHazardous Air Pollutant 
HCFCÑHydrofluorocarbons 
HClÑHydrogen Chloride 
HCPÑHabitat Conservation Plan 
HMRISÑHazardous Materials Incident Report System 
HRÑHour 
HSWAÑ Hazardous and Solid Waste Act 
HWCLÑ Hazardous Waste Control Law 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study xv 
HzÑ Hertz 
IEPRÑIntegrated Energy Policy Report 
IFRÑInternal Floating Roofs 
IMOÑ International Maritime Organization 
IPCCÑIntergovernmental Panel on Climate Change 
ISÑInitial Study 
ISBLÑInside Battery Limits 
ISGOTTÑ International Safety Guide for Oil Tankers and Terminals 
IS/MND Ð Initial Study/Mitigated Negative Declaration 
ISPSÑ International Ship and Port Facility Security 
ISRÑ Indirect Source Review 
ITÑInformation Technology 
ITOPFÑ International Tanker Owners Pollution Federation Ltd 
KGalÑOne Thousand Gallons 
kPaÑKilo Pascals 
KOPÑ Key Observation Point 
KVÑ Kilo Volt 
KWÑKilo Watt 
LBÑPound 
LDARÑLeak Detection and Repair Program 
LdnÑDay/Night Equivalent (sound measurement) 
LeqÑ Equivalent Continuous Sound Pressure Level 
LORSÑLaws, Ordinances, Regulations, and Standards 
LOSÑLevel of Service 
LOXÑLiquid Oxygen 
LUSTÑLeaky Underground Storage Tank 
MARSECÑ Maritime Security 
MBTAÑMigratory Bird Treaty Act 
MCCÑMotor Control Center 
MCEÑMaximum Credible Earthquake 
MEIÑMaximum Exposure Individual 
MeOHÑMethanol 
MND Ð Mitigated Negative Declaration 
MGDÑ Million Gallons per Day 
MOTEMSÑMaritime Oil Terminal Engineering and Maintenance Standards 
MOUÑ Memorandum of Understanding 
MPAÑ Marine Preservation Association 
MRSCÑ Marine Spill Response Corporation 
MRZÑ Mineral Resource Zones 
MS4Ñ Municipal Separate Storm Sewer System 
MSDSÑMaterial Safety Data Sheet 
MSLÑMean Sea Level 
MTSAÑ Maritime Transportation Security Act 
MUDÑ Stockton Municipal Utilities Department 
MWÑMega Watt 

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Endicott Biofuel Production Facility Project November 2013 
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Na. RCÑ National Research Council 
NAAQSÑNational Ambient Air Quality Standards 
NAHCÑ Native American Heritage Commission 
NaHOÑSodium Hydroxide 
NaOHÑSodium Hydroxide 
NCRÑNatural and Cultural Resources 
NFPAÑNational Fire Protection Association 
NHPAÑNational Historic Preservation Act 
NIHÑ National Institute of Health 
NIOSHÑNational Institute for Occupational Safety and Health 
NMFSÑ National Marine Fisheries Service 
NOD Ð Notice of Determination 
NOIÑ Notice of Intent 
NOxÑNitrogen Oxides 
NO2ÑNitrogen Dioxide 
NOAAÑ National Oceanic and Atmospheric Administration 
NPDESÑ National Pollutant Discharge Elimination System 
NPLÑ National Priorities List 
NPSÑ Non-Point Source 
NRCÑ National Response Center 
NTSBÑNational Transportation Safety Board 
O3ÑTrioxygen 
OCIMFÑ Oil Companies International Marine Forum 
OESÑ Office of Emergency Services 
OGVÑ Ocean Going Vessels 
OPA 90ÑOil Pollution Act of 1990 
OSBLÑOutside Battery Limits 
OSCÑOn-Scene Coordinator 
OSCPÑ Oil Spill Contingency Plan 
OSHAÑOccupational Safety Health Administration 
OSPRÑ Office of Oil Spill Prevention and Response 
OSROÑOil Spill Removal Organizations 
OSRPÑ Oil Spill Response Plan 
OVHDsÑ Overheads 
PbÑLead 
PCE Ð Passenger Vehicle Equivalent 
PFSÑPublic Facilities and Services 
PG&EÑ Pacific Gas and Electric 
PLCÑProgrammable Logic Controller 
PMÑParticulate Matter 
PM2.5ÑFine Particulate Matter 
PM10ÑRespirable Particulate Matter 
PortÑPort of Stockton 
PPMÑParts Per Million 
POTWÑPublicly Owned Treatment Works 

Table of Contents 
Endicott Biofuel Production Facility Project November 2013 
Initial Study xvii 
PSIÑPounds Per Square Inch 
PTÑ Port Zoning Classifications 
PRCÑCalifornia Public Resources Code 
RACTÑReasonably Available Control Technology 
RCRAÑ Resource Conservation and Recovery Act 
RCRA-LQGÑ Resource Conservation and Recovery Act Large Quantity Generator 
RCRA-SQGÑ Resource Conservation and Recovery Act Small Quantity Generator 
RECÑ Recognized Environmental Condition 
RFAÑRefined Fatty Acid 
RFS2ÑRenewable Fuels Standard 
RMPÑ Risk Management Plan 
ROGÑReactive Organic Gasses 
ROWÑRight of Way 
RRCEÑ Reduction, Recycling, and Reuse Element 
RSPAÑ Research and Special Programs Administration 
RTTMÑ Real Time Transient Model 
RVPÑReid Vapor Pressure 
RWCFÑ Stockton Regional Wastewater Control Facility 
RWQCBÑ Regional Water Quality Control Board 
SBÑSenate Bill 
S6O2ÑHexasulfur Dioxide 
S7O2ÑHeptasulfur Dioxide 
SCADAÑSupervisory Control and Data Acquisition 
SCHÑState Clearinghouse 
SCPÑSource Control Program 
SDSÑ Port of StocktonÕs Stormwater Development Standards 
SEÑ State Endangered 
SFDÑ Stockton Fire Department 
SIPÑState Implementation Plans 
SJCEHDÑSan Joaquin County Environmental Health Department 
SJCOGÑ San Joaquin Council of Government 
SJMSCPÑ San Joaquin County Multi-species Habitat Conservation Plan 
SJVAPCDÑ San Joaquin Air Pollution Control District 
SnO2ÑTin Dioxide 
SOCMIÑSynthetic Organic Compound Manufacturing Industry 
SO2ÑSulfur Dioxide 
SO3ÑSulfur Trioxide 
SOxÑSulfur Oxide 
SPCCÑ Spill Prevention, Control, and Countermeasures Plans 
SRÑ State Rare 
SRREÑ Source Reduction and Recycling Element 
SRWCFÑ Stockton Regional Wastewater Control Facility 
STÑState Threatened 
STARÑ Spill Team Area Responders 
SSOÑ Ship Security Officer 

Table of Contents 
Endicott Biofuel Production Facility Project November 2013 
Initial Study xviii 
SWPPPÑStorm Water Pollution Prevention Plan 
SWQCBÑState Water Quality Control Board 
SWRCBÑState Water Resources Control Board 
TACÑ Toxic Air Containment 
Targa Ð Targa Terminal, LLC 
TDSÑTotal Dissolved Solids 
TFVÑThreshold Friction Velocity 
TMDLÑ Total Maximum Daily Load 
TOPÑTake Over Point 
TRCÑ TRC Solutions, Inc. 
TRISÑToxic Chemical Release Inventory System 
TSAÑ Transportation Security Administration 
TSDÑTreatment, Storage, and Disposal Facilities 
TSPÑTerminal Security Plan 
TWICÑ Transportation Worker Identification Credential 
UBCÑUniform Building Code 
UFCÑ Uniform Fire Code 
ULSDÑUltra Low Sulfur Diesel 
UNFCCCÑUnited Nations Framework Convention on Climate Change 
UNSÑUnified Numbering System 
USCÑUnited States Code 
USCGÑUnited States Coast Guard 
USDAÑUnited States Department of Agriculture 
USGSÑUnited States Geological Survey 
USFWSÑUnited States Fish and Wildlife Service 
VÑVolt 
ValleyÑSan Joaquin Valley 
VDEÑVisible Dust Emissions 
VOCÑVolatile Organic Compounds 
VRUÑ Vapor Recovery Unit 
VTSÑ Vessel Traffic Service 
WDRÑWaste Discharge Report 
WQCPÑ Water Quality Control Plan 
XSÑExtra Strong 

1.0 Introduction 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 1-1 
1.0 INTRODUCTION 
This Initial Study and proposed Mitigated Negative Declaration have been prepared under the 
direction of the Stockton Port District (Port), the Lead Agency under the California 
Environmental Quality Act (CEQA), for the Endicott Biofuels II, LLC (Endicott) Endicott 
Biofuel Production Facility Project. Endicott is proposing to develop a biofuel production facility 
on approximately 4.91 +/- acres on a parcel just north of the intersection at West Washington 
Street and Navy Drive, Assessor Parcel Number 145-02-007, within the Port of Stockton, 
Stockton, California. Endicott proposes to construct and operate a biofuel production facility 
with the capacity of 1,428,527 million barrels of biofuel annually. The proposed biofuel 
production facility will convert various feedstocks, via a process known as esterification free 
fatty acids, to a high quality, biodegradable fuel (Biofuel/B100) that will meet the American 
Society for Testing and Materials (ASTM) D6751 - 12 Standard Specification for Biofuel Fuel 
Blend Stock (B100) for Middle Distillate Fuels. The Endicott biofuels will be quality standard 
biofuels for use as a safe, cleaner and sustainable alternative to petroleum diesel. 
In addition to the proposed biofuel production facility, Endicott will be contracting with Targa 
Terminals, LLC, located across Navy Drive to the south from the proposed biofuel production 
facility for storage and pipeline services to store and transport fatty acid feedstock, fatty acid 
methyl esters (FAME)/B100, glycerin, pitch, and methanol. Targa will also provide Endicott 
with marine transport services from Berth #9, manifest rail rack and truck rack services from the 
Targa Terminal to move fatty acid feedstock, FAME/B100, glycerin, pitch, and methanol to and 
from the biofuel production facility and the marketplace. See Figure 1.0-1 for Vicinity and 
Location Map of the Lease Area for the proposed Endicott Biofuel Production Facility Project 
Area and See Figure 1.0-2 for the Biofuel Facility, Pipelines, Truck Rack, Rail Rack, Berth #9 
and Storage Facilities Map. 
This Initial Study and proposed Mitigated Negative Declaration have been prepared to identify 
and assess the anticipated environmental impacts of constructing and operating the proposed 
Endicott Biofuel Production Facility Project. This Initial Study analyzes the potential impacts of 
the proposed Endicott project with regard to the following environmental topic areas: (1) 
Aesthetics, (2) Agricultural and Forestry Resources, (3) Air Quality, (4) Biological Resources, 
(5) Cultural Resources, (6) Geology and Soils, (7) Greenhouse Gas Emissions, (8) Hazards and 
Hazardous Materials, (9) Hydrology and Water Quality, (10) Land Use and Planning, (11) 
Mineral Resources, (12) Noise, (13) Population and Housing, (14) Public Services, (15) 
Recreation, (16) Transportation and Traffic, (17) Utilities and Service Systems, and (18) 
Mandatory Findings of Significance. 
The Stockton Port District has reviewed the proposed Endicott project and has determined that 
the proposed project, with mitigation measures, as identified in the attached Initial Study, will 
not have a significant effect on the environment. Thus, an Environmental Impact Report (EIR) is 
not required pursuant to the California Environmental Quality Act (CEQA) of 1970 (Sections 
21000, et seq., Public Resources Code of the State of California). 

1.0 Introduction 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 1-2 
The initial study is a public document used by the decision making lead agency to determine 
whether a project may have a significant effect on the environment. If the lead agency finds 
substantial evidence that any aspect of the project, either individually or cumulatively, may have 
a significant effect on the environment, regardless of whether the overall effect of the project is 
adverse or beneficial, the lead agency is required to prepare an to analyze the issues at hand. In 
reviewing the site-specific information provided for the above-referenced project, the Stockton 
Port District found no substantial evidence that the Endicott project or any of its aspects might 
cause a significant effect on the environment, and consequentially a mitigated negative 
declaration is the proposed CEQA document for this project. 

1.0 Introduction 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 1-5 
All mitigation measures as identified in the projectÕs Initial Study, as well as all project 
components described in the Initial Study, are included in the Approval and incorporated into the 
project. The development and operation of the proposed biofuel production facility is a permitted 
use within the zoning classification of the lease area, Port (PT), and the lease area is designated 
as an Industrial land use by the City of Stockton 2035 General Plan. 
The Stockton Port District is soliciting views of interested persons and agencies on the content of 
the environmental information presented in this document. Due to time limits mandated by state 
law, your responses must be sent at the earliest possible date, but no later than the 30-day review 
period ending on December 18, 2013. 
Written responses should be sent to: 
Mr. Jason Cashman, Environmental Specialist 
Stockton Port District 
2201 West Washington Street 
P.O. Box 2089 
Stockton, CA 95201 
Phone: (209) 946-0246 
Fax: (209) 464-1251 
jcashman@stocktonport.com 

2.0 Environmental Review and Approval 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 2-1 
2.0 ENVIRONMENTAL REVIEW AND APPROVAL 
2.1 Regulatory Guidance 
This Initial Study/Mitigated Negative Declaration (IS/MND) has been prepared by the Stockton 
Port District to evaluate potential environmental effects of the proposed Endicott Biofuel 
Production Facility project, located on a 4.91 +/- acre parcel at the intersection of West 
Washington Street and Navy Drive, Assessor Parcel Number 145-02-007, within the Port of 
Stockton, Stockton, California. This document has been prepared in accordance with the 
California Environmental Quality Act (CEQA) (Public Resources Code Section 21000 et seq.) 
and the State CEQA Guidelines (California Code of Regulations [CCR] Section 15000 et seq.). 
An Initial Study (IS) is prepared by the Stockton Port District as lead agency to determine if the 
Endicott project may have a significant effect on the environment (State CEQA Guidelines 
Section 15063[a]) and to determine the appropriate environmental document. In accordance with 
CEQA Guidelines Section 15070, a Òpublic agency shall prepare É a proposed negative 
declaration or mitigated negative declaration É when: (a) The Initial Study shows that there is 
no substantial evidence É that the project may have a significant impact upon the environment, 
or (b) The Initial Study identifies potentially significant effects but revisions to the project plans 
or proposal are agreed to by the applicant and such revisions would reduce potentially significant 
effects to a less-than-significant level.Ó In this circumstance, the Stockton Port District as the 
lead agency has prepared a written statement describing its reasons for concluding that the 
proposed Endicott project would not have a significant effect on the environment and, therefore, 
does not require the preparation of an Environmental Impact Report (EIR). This IS/MND 
conforms to these requirements and to the content requirements of CEQA Guidelines Section 
15071. 
This IS/MND evaluates the environmental effects of the proposed Endicott Biofuel Production 
Facility Project. This IS/MND formalizes the Stockton Port DistrictÕs preliminary analysis to 
determine whether an EIR or Negative Declaration must be prepared. The IS/MND is based 
upon the CEQA Guidelines checklist which illuminates the various environmental impacts which 
may result from development. The checklist, however, is only part of the IS/MND. The IS/MND 
also explains the reasons for supporting the checklist findings and notes or references the sources 
or content of the data relied upon in its preparation as called for by (Sundstrom v. County of 
Mendocino (1988) 202 Cal.App.3d 296). At the same time, keep in mind that the IS is not 
intended to provide the full-blown analysis expected of a complete EIR (Leonoff v. Monterey 
County Board of Supervisors (1990) 222 Cal.App.3d 1337 and San Joaquin Raptor/Wildlife 
Rescue Center v. County of Stanislaus (1996) 42 Cal.App.4th 608). 
This IS/MND includes specific technical studies which examine the potential significance of an 
anticipated environmental effect. It also includes references to previous environmental 
documents or other information sources. This IS/MND is a crucial part of the record supporting 
the Stockton Port District's determination to prepare a Mitigated Negative Declaration. 

2.0 Environmental Review and Approval 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 2-2 
CEQA requires that the Lead Agency, through an IS, review the whole of a project. A project 
must not be broken into smaller parts, each of which alone might qualify for a Negative 
Declaration, in an attempt to avoid preparing an EIR (Association for Sensible Development of 
Bishop Area v. County of Inyo (1985) 172 Cal.App.3d 151). The decision to prepare an MND 
must be grounded in an objective, good faith effort on the part of the Lead Agency to review the 
project's potential for significant impacts (Sundstrom v. County of Mendocino, supra). 
An MND is subject to the consultation and notice requirements as follows (see Sections 21080.3, 
21091, and 21092 for details on current requirements). The Stockton Port District will consider 
the comments it receives during the review period (30 days) prior to adopting the proposed 
MND. If these comments include substantial evidence that a potential environmental effect may 
occur despite the project revisions or mitigation measures included in the MND, the Stockton 
Port District will either require further revisions to the proposed Endicott project which would 
effectively avoid or mitigate that effect, or if that is not possible, prepare an EIR. If new 
mitigation measures are required to the project after the 30 day review period and response to 
comments, the Stockton Port District will recirculate the revised MND for review prior to acting 
on the proposed Endicott project and adopting the document. This ensures that the public will 
have been afforded the chance to review the new mitigation measures as well as the revised 
project (Leonoff v. Monterey County Board of Supervisors (1990) 222 Cal.App.3d 1337 and 
Perley v. County of Calaveras (1982) 137 Cal.App.3d 424). Endicott must have agreed to or 
made the additional project changes before the MND is recirculated. 
Upon adopting a Mitigated Negative Declaration, the Stockton Port District must make both of 
the following findings: 
1. Revisions in the project plans or proposals made by, or agreed to by, Endicott before the 
proposed MND and IS are released for public review would avoid the effects or mitigate 
the effects to a point where clearly no significant effect on the environment would occur. 
2. There is no substantial evidence in light of the whole record before the public agency that 
the proposed Endicott project, as revised, may have a significant effect on the 
environment. (Sections 21064.5 and 21080(c)). 
The purpose of this IS is to evaluate the potential environmental impacts of the proposed 
Endicott project to determine what level of additional environmental review, if any, is 
appropriate. An MND has been prepared because the IS illustrated that there is no substantial 
evidence, in light of the whole record, that the proposed Endicott project as revised through 
required mitigation may have a significant effect on the environment. 
2.2 Scope of Initial Study 
Based on the analysis presented in this IS, it has been determined that the proposed Endicott 
project and adjacent support facilities provided by Targa would not result in any potentially 
significant impacts that cannot be mitigated to a less-than-significant impact. The analysis 
contained in this IS concludes that the proposed Endicott project would result in the following 

2.0 Environmental Review and Approval 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 2-3 
categories of impacts, depending on the environmental issue involved: no impact, less-thansignificant 
impact, less-than- significant impact with incorporation of Endicott project specific 
mitigation measures. Under these circumstances the preparation of an MND is appropriate. 
Since none of the conditions described in CEQA or the CEQA Guidelines calling for preparation 
of an EIR have occurred, this Initial Study includes mitigation measures to reduce all identified 
potential impacts of the Endicott project to a less than significant level. The analysis in this IS 
supports the proposed adoption of an MND. 
2.3 Public Agency and Review 
This Draft IS and proposed MND will be circulated for public and agency review from 
November 18, 2013 to December 18, 2013. Copies of the Draft Initial Study are available during 
normal operating hours at the Stockton Port District, 2201 West Washington Street, Stockton, 
CA. Comments on this Draft Initial Study must be received by 5 p.m. on December 18, 2013 and 
may be emailed to jcashman@stocktonport.com or mailed to: 
Mr. Jason Cashman, Environmental Specialist, III 
Stockton Port District 
2201 West Washington Street 
P.O. Box 2089 
Stockton, CA 95201 
Phone: (209) 946-0246 
Fax: (209) 464-1251 
jcashman@stocktonport.com 
The IS/MND is being circulated for public review and comment for a review period of 30 days. 
After comments are received from the public and reviewing agencies, Stockton Port District will 
consider those comments and may (1) adopt the MND and approve the proposed project; (2) 
undertake additional environmental studies and require additional mitigation measures; (3) 
require an EIR; or (4) reject the project. If the project is approved, Stockton Port District will be 
responsible for enforcing all mitigation measures. 
After public review of the IS/MND, the proposed Endicott project will be considered by the 
Stockton Port District, Board of Commissioners. A date for the public hearing has not yet been 
set. 
Should you wish to challenge the environmental document in court, you may be limited to 
raising only those issues you or someone else raised in written correspondence delivered to the 
Port Board of Commissioners, or in a public hearing on the proposed Endicott project. 

2.0 Environmental Review and Approval 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 2-4 
2.4 Project Information 
Project Title: Endicott Biofuel Production Facility Project 
Project Location: North of the intersection of West Washington Street & Navy Drive, Assessor 
Parcel Number 145-02-007, Stockton, California 
Lead Agency Name and Address: Stockton Port District, 2201 West Washington Street, 
Stockton, CA 95201 
Project SponsorÕs Name and Address: 
Endicott Biofuels, LLC 
2 Northpoint Drive, Suite 950 
Houston, Texas 77060 
Contact Persons and Phone Numbers: 
Mr. Stephen W. Brown, Principal & Board Member 
Endicott Biofuels, LLC 
2 Northpoint Drive, Suite 950 
Houston, TX 77060 
(713) 909-2230 
steve@endicottbiofuels.com 
Mr. Christopher J. Frantz, Principal 
Endicott Biofuels, LLC 
2 Northpoint Drive, Suite 950 
Houston, TX 77060 
(281) 598-2180 
chris@endicottbiofuels.com 
www.endicottbiofuels.com 
Location of the Administrative Record for this Project: Stockton Port District, 2201 West 
Washington Street, Stockton, CA 95201 
2.5 Organization of the Initial Study 
This Initial Study is organized into the following sections. 
Section 1.0 - Introduction: Provides summary background information about the proposed 
Endicott project, including project location, lead agency, and contact information. 
Section 2.0 - Environmental Review and Approval: Includes regulatory guidance of CEQA, 
purpose of the IS, the scope of the IS, public and agency review information, and an overview of 
the document's organization. 
Section 3.0 - Project Description: Includes a description of the proposed Endicott project. 

2.0 Environmental Review and Approval 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 2-5 
Section 4.0 - Environmental Factors Potentially Affected: Identifies which environmental 
areas, if any, the proposed Endicott project would cause ÔPotentially Significant ImpactsÕ as 
indicated by the analysis provided in the CEQA Environmental Checklist. 
Section 5.0 - Determination: Indicates whether impacts associated with the proposed Endicott 
project are significant, and what, if any, additional environmental documentation is required. 
Section 6.0 - Evaluation of Environmental Impacts: Contains the Environmental Checklist 
form for each resource area. The checklist is used to assist in evaluating the potential 
environmental impacts of the proposed Endicott project. The checklist identifies potential project 
effects as follows: (1) New Potentially Significant Impacts; (2) Less-Than-Significant impacts 
with Mitigation Incorporated; (3) Less-Than-Significant; (4) No Impact. This section also 
contains an explanation of all checklist answers and recommended mitigation measures. 
Section 7.0 Ð Fish and Game Determination 
Section 8.0 - References: Lists references used in the preparation of this report. 
Section 9.0 - Agencies and Persons Consulted: Provides the names of individuals contacted in 
preparation of this document. 
Section 10.0 - Report Preparers: Lists the names of individuals who assisted in the preparation 
of this IS/MND. 
Appendix A Ð Proposed Mitigated Negative Declaration 
Appendix B Ð Mitigation Monitoring and Reporting Plan 
Appendix C Ð Lease Legal Description and Alta Survey 
Appendix D - Cultural Resources Documentation 
Appendix E Ð Air Quality Technical Information 
Appendix F Ð Phase I Environmental Assessment 
Appendix G Ð Geotechnical Report 
Appendix H Ð Preliminary Engineering Report 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-1 
3.0 PROJECT DESCRIPTION 
3.1 Project Name 
Endicott Biofuel Production Facility Project 
3.2 Proposed Action 
Endicott is requesting from the Stockton Port District to lease Port property of approximately 
4.91 +/- acres to construct and operate a biofuel production facility at a location near the 
intersection of Navy Drive and West Washington Street on Assessor's Parcel Number (APN) 
145-02-007, in the Port of Stockton (Port), Stockton, California. Endicott further desires to 
obtain a Letter of Agreement from Targa Terminals, LLC (Targa) whereby Targa will provide 
storage and transfer infrastructure to support the proposed Endicott Biofuel Production Facility. 
Endicott proposes an initial lease period of 25 years, with the option to extend the lease 
incrementally for an additional period of 25 to 30 years, to coincide the lease period with the life 
of the proposed facility. The proposed lease area would provide adequate space for the initial 
facility, as well as for future expansion, if needed. Endicott improvements would include: 
. Inside Battery Limits (ISBL): feedstock fat splitting equipment (pumps, drums, settling 
tanks, heat exchangers), sweet water treatment facilities (treatment chemical vessels, 
reaction vessels, filters, pumps, heat exchangers), glycerin refinement equipment (heat 
exchangers, pumps, distillation equipment, bleaching, and scrubbing vessels), pitch 
retrieval equipment (pumps, vacuum knockout pot) and fatty acid distillation and 
esterification facilities (esterification reactor, fatty acid column, methanol column, 
reaction and methanol re-boilers, fatty acid heaters, condenser, methanol recovery tanks, 
pre-heater, pumps, esterification catalyst drum wash tank, OVHDS distillate pot) 
. Outside Battery Limits (OSBL) Endicott Biofuel Production Facility: production tanks, 
secondary containment systems, piping, product pipelines, boilers, water cooling tower, 
thermal oxidizer, vapor control, nitrogen plant, compressor skids, a control, laboratory & 
administration building, stormwater runoff infrastructure improvements (bio retention 
basin), emergency shutdown system and other out buildings (pump, utilities, storage). 
Targa Terminal Storage and Transfer Support Facilities: storage tanks, pipelines, truck 
loading and unloading rack and canopy, rail loading and off-loading rack, Berth #9 
marine transfer facilities, a motor control center, fire protection, lighting, security, access 
and product off-site transport, stormwater runoff infrastructure improvements (bio 
retention basin), emergency shutdown system, and cathodic protection (See Figure 3.2-1: 
Endicott Biofuel Production Facility Site Plan). 
3.3 Required Permits and Approvals 
Many laws and policies have been adopted at the federal, State, and local levels to protect 
environmental resources and ensure that development is appropriately planned and managed. 
Table 3.3-1 summarizes the principal laws, regulations, and policies with which the proposed 
Endicott project must comply. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-3 
Table 3.3-1: Potentially Applicable Compliance and Review Requirements 
Resource Area Compliance Requirements 
Aesthetics ¥ Stockton 2035 General Plan 
¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.32.070 
¥ Stockton Municipal Code Title 2, Chapter 2.94, Stockton Arts Commission 
Agricultural Resources ¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.36.040, 
Agricultural Preservation 
¥ Stockton Municipal Code Title 16, Division 7, Chapter 16.236, Williamson 
Act Regulations 
Air Quality/Green House 
Gas 
¥ Federal Clean Air Act and Clean Air Act Amendments 1990 
¥ California Clean Air Act (Section 112(r)(1))ÑRequires the facility operator 
to identify hazards that may result from accidental releases 
¥ New Source Performance Standards (40 CFR 60) 
¥ New Source Performance Standards for Boilers of ³10 million BTU 
¥ New Source Performance Standards (40 CFR 60) 
¥ San Joaquin Valley Air Pollution Control District Plans 
¥ Stockton Municipal Code Title 16, Division 3, Chapters 16.32.040; 
16.32.090 
¥ San Joaquin Valley Air Pollution Control District, Authorities to Construct 
and Authorities to Operate 
Biology ¥ Federal and State Endangered Species Acts 
¥ Federal Migratory Bird Treaty Act 
¥ Federal Bald and Golden Eagle Protection Act 
¥ California Native Plant Protection Act 
¥ California Fish and Game Code 
¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.72.245, Heritage 
Trees 
¥ San Joaquin Council of Governments, Habitat Conservation Plan Permits 
Cultural Resources ¥ California Public Resources Code Sections 5024 and 5024.5 
¥ State Historic Preservation Office Requirements 
¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.36.050, Cultural 
Resources 
¥ Stockton Municipal Code Title 16, Division 7, Chapter 16.220, Cultural 
Resources 
Geology and Soils ¥ Stockton Municipal Code Title 15, Chapter 15.48, Grading and Erosion 
Control 
¥ City of Stockton, Grading Permit 
¥ Port of Stockton, Stormwater Development Standards Plan 
Hazards and Hazardous 
Materials 
¥ California Code of Regulations Title 22 
¥ California Hazardous Materials Release Response Plans and Inventory Act 
¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.36.080, 
Hazardous Materials 
¥ Stockton Municipal Code Title 12, Chapter 12.24, Lights on Obstructions in 
Public Streets 
¥ City of Stockton Office of Emergency Services, Hazardous Materials 
Business Plan and Hazardous Material Permit 
¥ San Joaquin County Environmental Health Department is the CUPA and 
regulates hazardous materials 
¥ California State Fire Marshal review of product pipeline design 
¥ DOT Hazardous Materials Regulations (amended by Homeland Security 
Act of 2002)ÑRequires the Implementation of a HM 232 hazardous 
materials plan 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-4 
Resource Area Compliance Requirements 
¥ Oil Pollution Act of 1990 (OPA 90) 
¥ EPA Emergency Planning and Community Right to Know Act (EPCRA) 
Hazardous Materials Plans (Section 304, 311, 312, 313) 
¥ U.S. Environmental Protection Agency letter of approval for Facility 
Response Plan 
Hydrology and Water 
Quality 
¥ Federal Clean Water Act 
¥ Porter-Cologne Water Quality Control Act 
¥ California Department of Health Services requirements for potable water 
facilities 
¥ Stockton Municipal Code Title 13, Chapter 13.16, Stormwater Management 
and Discharge Control 
¥ Stockton Municipal Code Title 15, Chapter 15.48, Grading and Erosion 
Control 
¥ State Water Resources Control Board, Aboveground Storage Tank Program 
and General Industrial Activity Stormwater Permits 
¥ California Regional Water Quality Control Board, Construction Activities 
Stormwater General Permit 
¥ California Regional Water Quality Control Board, Industrial Activities 
Stormwater General Permit 
¥ Central Valley Regional Water Quality Control BoardÑNPDES and 
SWPPP 
¥ Federal Clean Water ActÑOil Spill Response Plan 
¥ 40 CFR 112 (Requirement for a Spill Preventions Control Countermeasure 
Plan) 
Land Use and Planning ¥ Stockton 2035 General Plan 
¥ Stockton Municipal Code Title 16, Division 2, Chapter 16.16, Zoning 
Districts Established, Zoning Map Adopted 
¥ Stockton Municipal Code Title 16, Division 2, Chapter 16.24, Zoning 
District Development Standards 
¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.36.110, Setback 
Regulations and Exceptions 
¥ Stockton Municipal Code Title 16, Division 7, Chapter 16.228, 
Nonconforming Uses, Structures and Parcels 
¥ California Government Code 
¥ Stockton Port District Lease Approval 
¥ City of Stockton building permits and encroachment permits 
Mineral Resources ¥ California Surface Mining and Reclamation Act of 1975 
Noise ¥ Stockton 2035 General Plan 
¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.60, Noise 
Standards 
¥ Stockton Municipal Code Title 8, Chapter 8.20, Noise Regulations 
Population and Housing ¥ Stockton 2035 General Plan 
¥ Stockton Housing Element 
¥ Regional Housing Allocation Plan 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-5 
Resource Area Compliance Requirements 
Public Services and Utilities ¥ Stockton 2035 General Plan 
¥ Environmental Enforcement and Training Act of 2002 
¥ Stockton Municipal Code Title 15, Chapter 15.12, Fire Code 
¥ California Education Code Sections 52080-52086 
¥ Stockton Municipal Code Title 11, Chapter 11.24, State Video Service 
Franchises 
¥ Stockton Municipal Code Title 11, Chapter 11.04, Electric Franchise 
¥ Stockton Municipal Code Title 11, Chapter 11.12, Telephone Franchise 
¥ City of Stockton, Industrial Waste Discharge Permit 
Recreation and Open Space ¥ Stockton 2035 General Plan 
Transportation/Traffic ¥ Stockton 2035 General Plan 
¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.36.030, Access, 
General 
¥ Stockton Municipal Code Title 16, Division 3, Chapter 16.36.140, Traffic 
Sight Area 
¥ Stockton Municipal Code Title 10, Chapter 10.04, Traffic Regulations 
¥ Stockton Municipal Code Title 10, Chapter 10.08, Routes For Commercial 
Vehicles and Vehicles Transporting Flammable Liquids 
Biofuel Specific 
Regulations 
¥ EPAÕs Renewable Fuels Standards (RFS2) Program under 40 CFR 80 
Subpart M 
¥ Registration with EPAÕs Fuel and Fuel Additive Registration Systems (form 
3520-12) 
¥ Facility Response Plan rule for Animal Fat/Vegetable Oil Facilities in 40 
Code of Federal Regulations (CFR) 112 and 33 CFR154 
¥ Toxic Substance Control Act regulation of Biotechnology microorganism 
utilized in the creation of biofuels under 40 CFR 725.1 
¥ CARB GHG annual inventory documentation (to be submitted to CARBÑ 
17 CCR 95121) 
¥ IRS Form 637 (Excise Taxation form for certain activities) 
¥ Weigh master permit and certification of scales 
¥ Registration with California State Board of Equalization (Forms BOE-501- 
DD and BOE-506-PO) 
¥ RCRA Contingency Plan: 40 CFR 264.50-264.56ÑPrepared by owners and 
operators of permitted hazardous waste treatment, storage, and disposal 
facilities; must be submitted to EPA Regional Administrator 
¥ ASTM D 6571: Standard Test Method for Determination of Biodiesel (Fatty 
Acid Methyl Esters) Content in Diesel Fuel Oil Using Mid Infrared 
Spectroscopy (FTIR-ATR-PLS Method) 
¥ ASTM 6584: Standard Test Method for Determination of Total 
Monoglycerides, Total Diglycerides, Total Triglycerides, and Free and 
Total Glycerin in B-100 Biodiesel Methyl Esters 
¥ ASTM 7371: Standard Test Method for Determination of Biodiesel (Fatty 
Acid Methyl Esters) Content in Diesel Fuel Oil Using Mid Infrared 
Spectroscopy (FTIR-ATR-PLS Method 
¥ ASTM EN 14538: Potassium and Sodium by Spectrometric Analysis 
¥ ASTM D2500: Cloud and Pour Point 
¥ ASTM D445: Viscosity 
¥ ASTM D664: Total Acid Number (TAN) 
¥ ASTM D2709: Water and Sediment 
¥ ASTM D1160 Distillation, 90 % Recovery 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-6 
3.4 Background and Context 
Endicott is proposing the construction of a biofuel production facility on land owned by the 
Stockton Port District (Port). The lease area is located near the intersection of Navy Drive and 
West Washington Street at APN 145-02-007, Stockton, California. The proposed lease area 
consists of approximately 4.91+/- acres adjacent to the existing TXI-Riverside Cement facility 
(see Appendix C: Lease Legal Description and ALTA Survey). The proposed Endicott project is 
planned to include a biofuel production facility with the ability to refine and process a variety of 
lipid feedstocks into fatty acid methyl esters (FAME) and the ability to refine the 
byproducts/effluents associated with these diverse feedstocks into marketable products (Glycerin 
and Pitch). The biofuel production facility is designed to accommodate the following output and 
input volumes: 
Table 3.4-1: Biofuel Production Facility Input/Output Volumes 
Material Barrels Per Day Gallons Per Day 
Input 
Fatty Acid Feedstock 4,838 203,818 
Methanol (MeOH) 588 24,640 
Output 
Pitch 428 17,992 
Glycerin 388 16,303 
FAME (B100) 4,290 180,163 
Data presented in this document reflect relevant data from conceptual plant renderings based on 
existing, equivalent biofuel production facilities. These production models were used to 
determine potential impacts in accordance with CEQA guidelines. Endicott Biofuels, LLC 
employs a proprietary, cutting edge process to produce pure biofuel in a manner that exceeds 
traditional production efficiencies which utilizes esterification as the main reaction mechanism. 
EndicottÕs processes are detailed in and protected by United States Patent numbers 8105398, 
8105399, 8123822, and 8449629. The final facility design would ultimately be provided by 
Endicott; exact input/output consumption values may vary from assumed values provided herein 
for purposes of CEQA evaluation. 
The proposed biofuel production facility would be equipped to receive a variety of feedstocks, 
natural fats and oils, and/or other inedible feedstocks from both domestic and foreign sources via 
marine and terrestrial modes utilizing loading/offloading-rack services administered by Targa 
Terminals for rail and tanker trucks at the adjacent Targa Terminal facility as well as barge 
services at the deep water channel Berth #9. Modifications to the Targa loading/offloading-rack 
installations would be necessary to accommodate the potential variety of lipid feedstocks which 
may be brought in for the proposed biofuel production facility, including boilers at each site 
which would supply steam to liquefy possible solid feedstocks such as grease or tallow within 
railcars, trucks, and marine vessels. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-7 
The potential feedstocks to be handled at the proposed Endicott biofuel production facility could 
vary widely due to the flexibility in EndicottÕs patented process. Feedstocks which may be 
utilized at the Endicott biofuel production facility include: algae oil, tallow, brown grease, choice 
white grease, poultry fat, used cooking oil, and yellow grease, as well as a wide variety of other 
plant/vegetable/biomass derived oils. EndicottÕs ability to make use of diverse materials which 
would otherwise destined to be disposed of as waste. Additional materials to be utilized at the 
proposed biofuel production facility would include nitrogen (to be produced on site); methanol; 
ferric chloride, sodium hydroxide, and hydrogen chloride for water treatment applications; and 
proprietary esterification catalysts (Davy Process Technology, Ltd). Materials produced at the 
biofuel production facility would include FAME (B100) to be shipped out for blending with 
traditional petroleum diesel or marketed as B100; pitch, a byproduct of fatty acid distillation 
similar to No.6 bunker fuel oil (ASTM D396); and glycerin, a byproduct of feedstock refinement 
(fat splitting) which would be refined on site. 
The Port would have primary jurisdiction over the proposed Endicott project and will act as the 
CEQA lead agency. The federal regulatory agencies that may have jurisdiction over this project 
include the U.S. Environmental Protection Agency (EPA), U.S. Army Corps of Engineers 
(Corps), and U.S. Fish and Wildlife Service (USFWS). State and local regulatory agencies 
involved in the permitting process include the State Water Quality Control Board (SWQCB), 
California Department of Fish and Wildlife (DFW), San Joaquin Valley Air Pollution Control 
District (SJVAPCD), City of Stockton (City), California Board of Equalization, and the Port. 
3.4.1. Project Need 
3.4.1.1. Changing Energy Policy 
Federal and State policy has called for increased use of renewable energy sources in 
transportation fuels. To comply with regulations mandated by the Energy Independence and 
Security Act of 2007; the Renewable Fuel Standard program; and California State Assembly Bill 
32 Low Carbon Fuel Standard, a drastic increase in biofuel infrastructure, including production, 
storage, distribution, and retail facilities, would be necessary to facilitate new blending 
requirements. According to the EPA, the Renewable Fuel Standard program will increase the 
volume of renewable fuel required to be blended into transportation fuel from nine (9) billion 
gallons in 2008 to thirty-six (36) billion gallons in 2022. California is the largest biofuel market 
in the United States. In addition to augmented storage capacity, the implementation of new fuel 
standards calls for increased transportation infrastructure to allow for the conveyance/handling of 
alternative fuel materials. A California Energy Commission (CEC) draft staff report titled 
Transportation Energy Forecasts and Analyses for the 2009 Integrated Energy Policy Report 
states ÒCurrently, the biodiesel infrastructure is inadequate to accommodate widespread 
blending of biodiesel even at concentrations as low as B5,Ó and anticipates that new regulations 
and increased demand will, Òrequire a sizable increase in the use of biodiesel and a 
commensurate development of the associated distribution infrastructure to ensure adequacy of 
diesel fuel supplies for California.Ó 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-8 
3.4.1.2. Biofuel Feedstock Feasibility 
The feasibility of biofuel as an affordable, low carbon alternative to traditional petroleum based 
diesel fuel is reliant on low cost, environmentally beneficial lipid feedstocks. EndicottÕs 
exclusive patented approach to biofuel production allows for conversion of any fat/oil or fatty 
acid feedstock and allows for production of up to 100% of fatty acids in a given fat/oil. 
EndicottÕs produces high quality biofuel which results in a >75% reduction in greenhouse gas 
emissions (as compared with petroleum diesel-- measured by its carbon intensity value) while 
maintaining a cost competitive with that of petroleum based fuels. In anticipation of possible 
future fluctuations in commodity markets, the production technology is also ready to process 
future feedstocks under development today, including algae oil and lipids from cell ethanol 
production. The Endicott process produces exceptionally high quality biofuel regardless of the 
feedstock, exceeding all the requirements of both ASTM D6751 and EuropeÕs EN 14214 
biodiesel standards. Key attributes of the product are its high purity and low contaminants. 
EndicottÕs ability to process any lipid, regardless of ph properties (neutral/acidic/base), provides 
Endicott the ability to adjust to the marketÕs price demands and conform to any foreseeable 
developments in the regulatory environment. EndicottÕs unique approach to biofuel production 
will result in the ability to adapt to changing technologies and markets and will assist the State 
and Federal governments in reaching current and future GHG emissions reductions. 
3.4.1.3. Endicott Meeting Sustainable Transportation Fuel Goals 
Californians require mobility to conduct their everyday lives and attend to their business needs, 
in fact, as the second highest worldwide consumer of gasoline and diesel, roughly half of the 
energy Californians consume is for transportation (CEC, 2007b). In order to promote cleaner fuel 
sources and diminish the influence of the volatile global commodity of petroleum based fuels on 
the California economy, the State Alternative Fuels Plan (CEC, 2007; CARB, 2007) asserts that 
ÒCalifornia must take [actions] to increase the use of alternative non-petroleum fuels in a 
manner that minimizes costs to California and maximizes the economic benefits of in-state 
production,Ó and calls for an across the board reduction in CaliforniaÕs consumption of 
petroleum based transportation fuels, mandating that by 2020 renewable fuel sources must 
account for 20% of all on road fuel consumption to be increased to 30% by 2030. The CEC 
stated further that ÒCalifornia must be innovative and aggressive in finding more ways to make 
increased efficiency, greater renewable fuel use, and smart land use planning the most desirable 
consumer optionsÓ (CEC, 2007b). Thus, the proposed Endicott project and patented 
technologies/processes would help meet CaliforniaÕs stated needs for transportation energy 
facilities by providing critical infrastructure called for in the CECÕs Integrated Energy Policy 
Reports since 2007. 
3.4.2. Project Objectives 
The overall Endicott project objectives are to meet State and federally mandated targets for 
renewable fuels and help to meet mandated transportation emissions targets. Specifically, the 
proposed Endicott project objectives include: 
¥ Construct a facility that would allow Endicott to take advantage of the availability of rail, 
highway, deep-water channel/dock facilities, and pipeline transportation systems at the Port. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-9 
¥ Construct a facility using Best Available Emission Control Technology (BACT) that would 
significantly reduce facility air emissions. 
¥ Construct a facility that would allow for future expansion to accommodate regional growth 
as the area population and demand for renewable transportation fuels increases. 
¥ Establish a state-of-the-art Biofuel Production Facility to assist California in meeting 
greenhouse gas (GHG) abatement targets, decreasing reliance on imported petroleum fuel. 
¥ Develop a Òstate-of-the-artÓ facility, thereby reducing the environmental and safety risks 
associated with transporting and handling of sustainable transportation fuels production 
materials. 
3.4.3. Development Process 
Endicott is in the preliminary design and environmental review process to obtain the Port lease 
for the proposed biofuel production facility site, and letter of agreement with Targa Terminals 
for storage and transfer support facilities. Endicott and the Port are focused on addressing the 
environmental issues as effectively as possible. The proposed Endicott project would incorporate 
a number of state-of-the-art design features to protect the environment, which includes the 
following: 
¥ The feedstock pretreatment/fat splitting process to be employed in Unit 1 allows Endicott 
to process a wider variety of feedstocks than traditional biofuel production facilities can 
accommodate. This flexibility means that thousands of tons of fats that would otherwise 
be destined for area landfills can be processed and refined into clean, renewable 
transportation fuel. 
¥ A nitrogen production plant is to be built on site to ensure that Endicott can produce and 
store its products in a safe and environmentally friendly manner. Blanketing storage and 
production tanks with a nitrogen gas barrier helps to ensure product purity and reduce the 
possibility of combustion and emissions. 
¥ Unit 6 of the proposed facility will allow Endicott to refine crude glycerin, a byproduct of 
lipid feedstock processing, into high purity glycerin. This will greatly reduce the amount 
of waste to be produced at this facility as compared to traditional biofuel production 
facilities. The additional revenue stream provided by the sale of refined glycerin will 
assure financial feasibility and benefit the local economy. 
¥ The proposed Endicott biofuel production facility would operate under a permit issued by 
the San Joaquin Valley Air Pollution Control District (SJVAPCD) that includes an 
emissions cap. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-10 
¥ The use of a state of the art thermal oxidizer on site to process plant exhaust will help to 
limit the release of volatile organic compounds and offensive odors at and around the site 
of the proposed Endicott facility. 
¥ The biofuel production facility will utilize existing and/or approved storage and transfer 
infrastructure to support the facility operations at the Port of Stockton offered by Targa 
Terminals, LLC, an existing Port Tenant. 
Initial estimates of the proposed biofuel production facilityÕs operations determine that annual 
biofuel output capacity would be roughly 60 million gallons or 1,428,571 barrels helping to meet 
regional demand for renewable fuel sources and helping to satisfy environmental regulations. 
Future production could potentially be expanded based on a number of factors, including future 
regulatory requirements, port tariffs, feedstock supplies, market fluctuations impacting price of 
renewable and/or traditional petroleum transportation fuels, and regional demand for renewable 
transportation fuels. 
3.4.4. Regional Context 
The proposed Endicott project is located in the eastern area of the Port adjacent to various 
industrial production installations and terminal facilities (See Figure 3.4-1: Regional Location 
Map and Figure 3.4-2: AssessorÕs Map). The Port consists of approximately 2,000 acres of land 
for industrial development. The Port is administered by the Stockton Port Commission under the 
legal authority of the California Harbors and Navigation Code, Chapter 2, Article 6240.3. The 
Stockton Port Commission is chartered to develop and operate the Port to benefit maritime uses, 
and it functions as a landlord by leasing Port properties to more than 100 tenants. The Port 
currently accommodates a biodiesel production facility on Rough and Ready Island and 
petroleum terminals for Targa, NuStar, Shell, Buckeye and Tesoro. The Port also contains 
alternative renewable fuels companies such as Pacific Ethanol and Community Fuels. The Port is 
located 75 nautical miles from the Golden Gate Bridge and 1 mile from Interstate 5. Rail service 
is provided by Central California Traction, Union Pacific and Burlington Northern Santa Fe 
Railroads. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-13 
3.4.5. Project Setting 
The proposed Endicott Biofuel Production Facility Project is located at the intersection of Navy 
Drive and West Washington Street in the Stockton Port District. The lease areaÕs shape is 
roughly triangular and is approximately 4.91 +/- acres in size within the parcel identified as San 
Joaquin County AssessorÕs Parcel Number (APN) 145-02-007. Adjacent to the subject property, 
are the following properties and associated land uses: Rough and Ready Island (also known as 
the PortÕs Western Complex) to the northwest across the San Joaquin River; the Stockton Police 
Department gun and pistol training range to the west; Pacific Ethanol production facility and 
Targa Terminal to the southwest; Yara North America terminal to the south; and, to the east, a 
rail spur and the TXI-Riverside cement production facility. The entire lease area is relatively 
unimproved, other than a groundwater monitoring well located near the roadway at the 
intersection of Navy Drive and West Washington Street. The terrain is primarily flat throughout 
the entire property with a very slight slope to the west/southwest toward Navy Drive. The entire 
property sits below the level of the levee which runs along the San Joaquin River along the 
northern edge of the property and the elevated portion of Navy Drive to the west which climbs to 
the height of the levee at the northern end of the property. See Figure 3.4-3: Project Setting 
shows the surrounding land uses.) 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-15 
3.5 Description of Project Facilities 
The following describes the major components of the proposed Endicott project: Endicott 
Biofuel Production Facility: ISBL, Control Building/Lab, Boiler at production site, Other 
Buildings, Production, Nitrogen Production, Thermal Oxidizer, Fire Protection, Lighting, 
Security, Emergency Shutdown System, and Stormwater Runoff Improvements. Targa Terminals 
Storage and Transfer Support Infrastructure: Storage Tanks, Deep-water channel Berth #9 
transfer infrastructure, Truck Rack, Rail Rack, Boiler at Berth #9, Boiler at Targa Storage site, 
Access and Product Off-site Transport, Emergency Shutdown System, Cathodic Protection, and 
a Stormwater Runoff Improvements. An overview of the proposed Endicott project elements is 
provided below along with the operational parameters. 
The storage and transfer facilities operated by Targa located at the Targa Terminal site and Berth 
#9 were previously permitted under the Targa Stockton Tiered Initial Study/Proposed Mitigated 
Negative Declaration, submitted to the State Clearinghouse on February 27, 2012, with SCH 
#2012022071 and adopted by the Stockton Port Commission May 7, 2012. 
3.5.1. Biofuel Production Facility (ISBL) 
The ISBL is located on the eastern portion of the proposed Port lease area. Endicott proposes to 
design the ISBL in a linear fashion for ease of operations, and maintenance. The ISBL has been 
strategically placed for safety and emergency response. The overall Endicott process features six 
individual production units. The following Figure 3.5-1 Biofuel Production Facility (ISBL) 
shows the ISBL as proposed to be constructed within the proposed Endicott Biofuel Production 
Facility. The following sections describe the process within the ISBL. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-17 
3.5.1.1. Unit 1: Fat Splitting Process 
The key aspect of the Endicott process is its ability to process a variety of lipid feedstocks into 
high quality biofuel. This flexibility ensures independence from the fluctuations of global 
commodity markets and limits demand on edible sources of fat/oil is made possible by the Fat 
Splitting process involved in Unit 1. In this step of the process, triglycerides present in the lipid 
feedstock are separated into their constituent parts, breaking fatty acid chains from the glycerol 
to which triglycerides are bonded. This is achieved by processing the crude feedstock, with 
water, through a series of pumps, vessels, and heat exchangers. The result is a supply of free 
fatty acids (FFAs) and a dilute solution of water and glycerin known as Òsweet water.Ó 
It is estimated that, under normal operating conditions, Unit 1 will process up to 61,050 pounds 
of lipid feedstock using the following resources: 9,162 pounds of high pressure (1000 PSI) 
steam, 4,275 pounds of low pressure (50 PSI) steam, 6,225 pounds of process water, 7 pounds of 
water treatment chemicals, 26,825 pounds of cooling water, and 12,261 pounds of natural gas per 
hour; 52 cubic feet of compressed air per minute; and 415 kilowatts of electricity. Outlet from 
Unit 1 consists of 56,238 pounds per hour of crude free fatty acids to be processed further in Unit 
5 and 42,787 pounds of sweet water per hour to be processed in Unit 2. 
Unit 1 consumptions rates for CEQA environmental base line analysis is as follows: 
Table 3.5-1: Unit 1 Consumption 
LB/HR 
Inlet: Lipid Feedstock 61,050 
Outlet: Crude Fatty Acids 56,238 
Sweet Water 42,787 
Utilities Units 
LB/HR KW CFM 
Steam (1000 psi) 9,162 
Steam (50 psi) 4,275 
Process Water 6,225 
Cooling Water1 26,825 
Water treatment chemicals 7 
Air 52 
Electricity 415 
Natural Gas 12,261 
1 Cooling water figures represented in theTables found in Section 3.5 are a one-time use consumption. Cooling 
water is utilized with a Òclosed loopÓ system that recirculates the water. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-18 
3.5.1.2. Unit 2: Sweet Water Processing 
Unit 2 will process the estimated 42,787 pounds of sweet water effluent from Unit 1. The sweet 
water treatment process will use 2,568 pounds of low pressure (50 PSI) steam, 563 pounds of 
process water, .6 pounds of water treatment chemicals, 2,928 pounds of natural gas, 43 pounds of 
ferric chloride (FeCl3), 64 pounds of sodium hydroxide (NaOH), 43 pounds of hydrogen 
chloride (HCl), 43 pounds of filter aid, and 43 pounds of silica per hour; 73 cubic feet of air per 
minute; and 58 kilowatts of electricity to produce 42,744 pounds of clean sweet water per hour to 
be further processed in Unit 3. Residual fatty acids are skimmed and removed producing an 
estimated total of 43 pounds per hour of waste. This waste will be removed to a sanitary landfill 
as solid waste. 
Unit 2 consumptions rates for CEQA environmental base line analysis is as follows: 
Table 3.5-2 Unit 2 Consumption 
LB/HR 
Inlet: Sweet Water 42,787 
Outlet: Clean Sweet Water 42,744 
Waste 43 
Utilities Units 
LB/HR KW CFM 
Steam (50 psi) 2,568 
Process Water 563 
Water treatment chemicals 0.6 
Waste Disposal 43 
Air 73 
Electricity 58 
Natural Gas 2,928 
50% Caustic 64 
37% Hydrochloric Acid 43 
Ferric Chloride 43 
Filter Aid 43 
Silica 43 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-19 
3.5.1.3. Unit 3: Water Evaporation from Sweet Water 
In Unit 3 the water is removed from the treated sweet water from Unit 2 via evaporation. The 
estimated 42,744 pounds per hour of treated sweet water runs through a series of heat 
exchangers, evaporators, pumps, and vessels to remove 6,841 pounds per hour of crude glycerin 
which will be further refined in Unit 6. The Evaporation process will use an estimated 11,118 
pounds of medium pressure (300 PSI) steam, 11,830 pounds of process water, 18,779 pounds of 
cooling water, 13 pounds of water treatment chemicals, 11,174 pounds of natural gas per hour; 
26 cubic feet of compressed air per minute; and 39 kilowatts of electricity. It is estimated that 
this unit will produce 2,000 pounds of wastewater effluent per hour. 
Unit 3 consumptions rates for CEQA environmental base line analysis is as follows: 
Table 3.5-3: Unit 3 Consumption 
LB/HR 
Inlet: Clean Sweet Water 42,744 
Outlet: Crude Glycerin 6,841 
Utilities Units 
LB/HR KW CFM 
Steam (300 psi) 11,118 
Process Water 11,830 
Cooling Water 18,779 
Wastewater 2,000 
Water treatment chemicals 13 
Air 26 
Electricity 39 
Natural Gas 11,174 
3.5.1.4. Unit 4: Fatty Acid Distillation 
The estimated 56,238 pounds per hour of free fatty acids attained through the hydrolysis process 
in Unit 1 are further refined in Unit 4 through vacuum distillation to remove remaining fatty 
acids and triglycerides not conducive to the esterification process to follow in Unit 5. The fatty 
acids and triglycerides removed in this process form a pitch to be sold as a material that is similar 
to No.6 heating oil (ASTM D396). Output from Unit 4 is projected to include 52,678 pounds per 
hour of refined free fatty acids and 3,559 pounds per hour of pitch. 
Estimated baseline consumption factors for the fatty acid distillation process are as follows: 
3,938 pounds of medium pressure (300 PSI) steam, 6,189 pounds of low pressure (50 PSI) 
steam, 319,972 pounds of thermal oil, 5,806 pounds of process water, 9,876 pounds of cooling 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-20 
water, 7 pounds of water treatment chemicals, 11 pounds of sodium hydroxide (NaHO), and 
27,956 pounds of natural gas per hour; 48 cubic feet of air per minute; and 153 kilowatts of 
electricity. 
Table 3.5-4: Unit 4 Consumption 
LB/HR 
Inlet: Crude Fatty Acids 56,238 
Outlet: Refined Fatty Acids 52,678 
Pitch 3,559 
Utilities Units 
LB/HR KW CFM 
Steam (300 psi) 3,938 
Steam (50 psi) 6,189 
Process Water 5,806 
Cooling Water 9,876 
Wastewater (POTW) 50.00 
Water treatment chemicals 7 
Thermal Oil 319,972 
Air 48 
Electricity 153 
Natural Gas 27,956 
Caustic 11 
3.5.1.5. Unit 5: Esterification 
In Unit 5, the 52,678 pounds per hour of refined free fatty acids from Unit 4 are combined with 
methanol and a catalyst in the esterification reactor to create 55,064 pounds per hour of fatty acid 
methyl esters (FAME/B100). By products of this process include an estimated 4,339 pounds per 
hour of water, 278 pounds per hour of excess methanol/dimethyl ether. 
Unit 5 consumption rates for CEQA environmental base line analysis is as follows: 2,715 pounds 
of medium pressure (300 PSI) steam, 21,540 pounds of low pressure (50 PSI) steam, 27,357 
pounds of process water, 44,073 pounds of cooling water, 31 pounds of water treatment 
chemicals, 6,324 pounds of methanol, and 27,285 pounds of natural gas per hour; 45 cubic feet 
of air per minute; and 134 kilowatts of electricity. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-21 
Table 3.5-5: Unit 5 Consumption 
LB/HR 
Inlet: Refined FFAs 52,678 
Outlet: Biofuel 55,064 
Water 4,339 
Utilities Units 
LB/HR KW CFM 
Steam (300 psi) 2,715 
Steam (66 psi) 21,540 
Process Water 27,357 
Cooling Water 44,073 
Wastewater (POTW) 4,339 
Water treatment chemicals 31 
Air 45 
Electricity 134 
Natural Gas 27,285 
Methanol 6,324 
3.5.1.6. Unit 6: Glycerin Refinement 
In Unit 6 the 6,841 pounds per hour of crude glycerin produced in Unit 3 is refined through a 
process which includes distillation, deodorizing, and bleaching aided by a series of pumps and 
heat exchangers. The crude glycerin which is a byproduct of the fat splitting in Unit 1 is refined 
to a point suitable for resale to be employed in a variety of uses. 
Unit 6 consumption rates for CEQA environmental base line analysis are as follows: 8,130 
pounds of medium pressure (300 PSI) steam, 615 pounds of low pressure (50 PSI) steam, 5,633 
pounds of process water, 7,447 pounds of cooling water, 6 pounds of water treatment chemicals, 
and 8,872 pounds of natural gas per hour; 45 cubic feet of compressed air per minute; and 400 
kilowatts of electricity. It is estimated that Unit 6 will produce 6,053 pounds of refined glycerin 
and 2,000 pounds of wastewater effluent per hour. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-22 
Table 3.5-6: Unit 6 Consumption 
LB/HR 
Inlet: Crude Glycerin 6,841 
Outlet: Refined Glycerin 6,054 
Utilities Units 
LB/HR KW CFM 
Steam (300 psi) 8,130.00 
Steam (50 psi) 615.00 
Process Water 5,633 
Cooling Water 7,442 
Wastewater (POTW) 2,000.00 
Water treatment 
chemicals 6 
Air 45 
Electricity 400 
Natural Gas 8,872 
3.5.2. Berth #9 (Targa Terminals to Provide Transfer Services to Endicott) 
3.5.2.1. Berth #9 
The proposed Endicott project does not require modification to Berth #9 not already discussed in 
TargaÕs Tiered Initial Study/Mitigated Negative Declaration, SCH #2012022071 (noted in 
Section 2.5). TargaÕs proposed improvements will sufficiently service EndicottÕs needs which 
include the transfer of up to 50% of EndicottÕs in bound feedstocks and outbound biofuel 
products. Such improvements include: 
. Ship to shore transfer equipment (booster pumps, flexible hoses, pipeline hatch/manifold, 
valves, control system, piping etc.); 
. FAME/B100 and fatty acid Pipeline(s) between Endicott, Berth #9, and TargaÕs facility; 
. Mooring equipment, fenders, to accommodate lipid feedstock and FAME/B100 barges 
and tankers; 
. Vapor control system; 
. Boiler to heat the barges and tankers to move lipid feedstocks; 
. Lipid feedstocks and FAME/B100 transfer pipes on Berth #9; and 
. Fire suppression system (Fire Water System, Foam System, and Compressed Air). 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-23 
The proposed biofuel/feedstock transfer infrastructure to be added to Berth #9 will comply with 
the EPA and USCG regulations such as the USCGÕs Facility Response Plan rule for Animal 
Fat/Vegetable Oil Facilities in 40 Code of Federal Regulations (CFR) 112 and 33 CFR154. 
The following number of daily vessel trips is expected to be generated to accommodate the 
transport of lipid feedstock and FAME through Berth #9 (estimated based on 10,000 bbl barge): 
Table 3.5-7: Barge Traffic 
Product Vessels per Day 
In Lipid Feedstock Less than 1 
Out Biofuel (FAME/B100) Less than 1 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-26 
3.5.2.2. FAME/Feedstock Transfer Infrastructure 
While FAME/B100 barges or lipid feedstock barges are in loading or off-loading mode, there 
will be a safety zone that encircles the subject vessel and extends onto Berth #9. Site specific 
safety protocols will be followed to provide maximum safety for the loading/off-loading 
processes. No cargo handling or passenger embarkation or disembarkation can be carried out 
within this safety zone during active loading or off-loading activities. The extent of the safety 
zone is determined at the discretion of the Port, although distance of 100 feet is common. 
In addition, Berth #9 will be outfitted with a boiler, which will be used to heat barges via a 
heating coil system, to assist in the offloading of fatty acid feedstocks into pipelines. This 
heating is necessary to ensure uninterrupted flow of feedstocks through pipelines. 
3.5.2.3. FAME/Feedstock Transmission Pipeline 
FAME and lipid feedstock transmission pipelines run between Targa tank storage facilities and 
Berth #9 and terminate dockside in the biofuel/feedstock hatches. The transmission pipelines will 
be installed below-ground and will be covered by a thick concrete slab encapsulated in a lowdensity 
concrete fill (also known as Controlled Low-Strength Material or CLSM). This lowdensity 
fill is easy to remove, allowing easy access to pipelines for repair, if damaged or if 
modifications are necessary. The fuel hatches (at Berth #9) will be covered with steel plates, 
when not in use, and would not impede cargo loading operations or proposed future operations at 
times when FAME/feedstock vessels are not in port. The FAME/feedstock transmission 
pipelines are proposed to be designed with flanges at the take-over-point (TOP) in the 
biofuel/feedstock hatches that connects the flexible ship-to-shore transfer hose. The vessels 
typically have the shipside loading and unloading pipe terminals amidships. Thus, connections, 
from vessel to the Berth #9 transmission pipelines will occur amid ship. 
In most instances, vessels would provide the required hydraulic pressure to pump the cargo from 
the vessel to the landside storage tanks by onboard pumps when in the unloading mode. A boiler 
will be located on Berth #9 to heat high viscous lipid feedstock. Heating such feedstocks will, 
allow the feedstocks to be properly pumped through the pipeline. 
Proposed safety features of the FAME/feedstock transfer pipeline include a flexible transfer hose 
and a typical shut-off valve. The flexibility of the hose will allow for the hose to be coiled 
and/or rolled and moved to a location of Berth #9 away from Berth # 9 operations (such a 
location may include a lay down area or an area within the Berth #9 transit shed which would be 
away from operations). The shut-off valve will be utilized to stop flow of product within the 
pipeline in the event of an emergency. 
Downstream of the FAME/feedstock hatch, the FAME/feedstock transfer pipes rest on pipe 
supports which would be attached to the underside of the concrete slab of Berth #9. This 
methodology allows for periodic external inspection of and ease of repairs to the 
FAME/feedstock pipelines. A small catch basin will be located under the pipeline to contain 
FAME/feedstock potential leaks into the water below. FAME and feedstock will each have a 
separate, dedicated line running between Berth #9 and Targa Storage. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-27 
3.5.2.4. Containment, Curbing, and Sump System 
All deck areas on Berth #9 that would be subject to potential leaks, spills, drips from equipment, 
pipe flanges, pumps, flexible hoses, and valves would be contained within a secondary 
containment system. Rainwater falling into this area would be collected and drained to a sump. 
Pumps would be installed to pump the sump water to the proposed Targa Terminal water 
treatment oil-water separator and discharged pursuant to a National Pollutant Discharge 
Elimination System (NPDES) permit. 
3.5.2.5. Piping, Pumps, and Valves 
Piping on Berth #9, within the Port and the Targa Terminal for lipid feedstock will be stainless 
steel Type 316L (UNS S31603) or 304L (UNS S30403). Piping for the FAME/B100 will be 
American Petroleum Institute (API) Spec 5L line pipe, standard XS wall. Pipe diameters have 
been estimated at between 6Ó and 16;Ó exact diameters will be determined as engineering is 
completed. Likewise, piping may be trenched or laid atop the ground (where appropriate). If 
trenched, pipelines will likely be set at depths of 5+ feet below ground surface, although actual 
depths will vary as appropriate. It is proposed that the following equipment may be utilized for 
product transfer from Berth #9: 150 (or greater) gallons per minute (gpm), 20 horsepower; 150 
psig discharge dockside pumps (for moving lipid feedstock and FAME/B100). Two additional 
pumps may be utilized to move FAME/B100 and lipid feedstocks from Berth #9 to the Tank 
Farm or from the Tank Farm to Berth #9. Proposed valves on Berth #9 include gate valves and 
fire water valves will the outside stem and yoke type. Check valves may be used on the various 
lines in the system to prevent backflow. 
3.5.2.6. Berth Fire Prevention, Detection, and Suppression System 
Per Facility Response Plan rule for Animal Fat/Vegetable Oil Facilities in 40 Code of Federal 
Regulations (CFR) 112 and 33 CFR154), a site specific Fire Protection Plan would be prepared 
as part of the Fire Hazards Analysis and Risk Assessment. Safety equipment proposed in the 
Fire Protection Plan will be incorporated into the final design. Such equipment would be 
designed in accordance with applicable Port, City, and State of California fire codes as well as 
the National Fire Protection Association (NFPA). Devices capable of detecting the presence of 
open flames (flame detectors) would be installed at Berth #9, if required by law or local 
ordinances. Flame detectors, if necessary, would be positioned to cover strategic areas such as 
the vicinity of motorized pumping areas and the berth loading dock. The flame detectors would 
be tied to a flame-detector control panel. Upon detection of a fire, the flame detectors would 
automatically trigger a fire alarm signal. 
3.5.3. Truck Rack (Targa Terminals to Provide Transfer Services to Endicott) 
The proposed Endicott project will utilize the truck racks located at Targa Terminals, across 
Navy Drive, to facilitate the loading/offloading of tanker trucks with trailers. The truck loading 
rack would be constructed of prefabricated steel to house an overhead pipeway. Each loading 
bay would be constructed of steel and include product metering and control equipment and 
loading arms. A berm would be constructed along the truck entrance and exit sides of the truck 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-28 
loading rack to prevent rainwater from entering the spill-containment area. Curbs would be 
constructed along the other sides of the truck loading rack. 
The truck rack may be supplied with steam from a boiler located at the Targa Terminal site to 
heat deliveries of lipid feedstocks for offloading to onsite storage tanks. In the alternative, steam 
may be supplied by other local sources, such as the DTE power plant located In order to meet 
plant production capacity, four truck bays will provide capacity for the off-loading of methanol 
and heated feedstock and the loading of glycerin, pitch, and biofuel (B100). It is estimated that 
roughly 25% of the lipid feedstocks and 50% of the methanol necessary for plant operations will 
arrive via the truck rack. Additionally, it is assumed that truck racks will be employed in the 
removal of roughly 50% of the glycerin and pitch which are byproducts of biofuel production, as 
well as 25% of the total biofuel production. 
In order to accommodate the transportation of the above stated materials, it is estimated that, 
based on the 25/25/50 loading ability described above, the following number of daily truck trips 
would be necessary (6000 gallon assumed truck capacity): 
Table 3.5-8: Estimated Truck Traffic 
Product Trucks per Day 
In Lipid Feedstock 9 
Methanol (MeOH) 2 
Out Biofuel (FAME/B100) 8 
Pitch 2 
Glycerin 2 
Pumps would be provided for loading/off-loading of each product to be conveyed through the 
truck rack. The pump would have a local start/stop push-button station for control. The tanks 
would all be equipped with a redundant high-level alarm (See Figure 3.5-4 Targa Terminal Site 
Plan for Endicott Storage and Transfer Improvements). 
3.5.4. Rail Rack (Targa Terminals to Provide Transfer Services to Endicott) 
The proposed Endicott project would utilize the Targa Terminal rail spur which is located at the 
northern end of the Pacific Ethanol and Targa sites across Navy Drive from the proposed 
Endicott project site including a railcar loading/off-loading system to facilitate the transfer of 
raw materials and finished products. A number 9 turnout would be installed on the port mainline 
just west of Navy Drive, giving access to the rail spur. The rail spur would continue west, 
crossing the driveway, then turn southwest, and run down between the existing Pacific Ethanol 
track and the driveway. As it runs in between the existing track and the driveway, another 
number 9 turnout would be employed, splitting the track into two parallel lines. These two 
tracks would be the end of the line, and would be for loading and unloading via rail racks. The 
southern split track would be 760 ft. long, allowing for 12 manifest rail cars, and the northern 
split track would be 740 ft. long, also allowing for 12 manifest rail cars. After the new rail line 
crosses the driveway, the line, the second number 9 turnout, and the split loading/unloading lines 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-29 
will be enclosed in a security fence. At the point that the rail spur crosses the driveway, a 
Goodyear rubber roadway crossing would be installed, making it easier to drive over for cars and 
trucks entering and exiting the Targa and Pacific Ethanol facilities. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-31 
The rail rack system could be expanded to load/offload additional products by adding 
supplementary pumps, product headers, and vapor recovery headers. The track would have pans 
and piping connections for 12 unloading positions. The rail off-loading rack would be 
constructed of pre-fabricated steel to support the pipeway. Each header would be constructed of 
steel and include product metering and control equipment. Pumps would be provided for the offloading 
of the rail cars to storage tanks with a local start/stop push-button station for controls. 
The storage tanks would have a redundant high-level alarm. 
It is estimated that roughly 25% of the lipid feedstocks and 50% of the plantÕs methanol supply 
would arrive via manifest railcar. Rail would also account for transportation of roughly 50% of 
the glycerin and pitch produced at the plant, as well as 25% of the total biofuel production. The 
rail spur will also be supplied with steam from a boiler located at Targa Terminal to be used to 
heat cars of lipid feedstock to allow for offloading to storage tanks. This is the same boiler that 
will be utilized for the truck rack, and tank heating as well (See Figure 3.5-4 Targa Terminal Site 
Plan for Endicott Storage and Transfer Improvements). 
It is estimated the following number of manifest railcars (estimated 25,000 gallon capacity each) 
will be needed daily for materials transportation: 
Table 3.5-9: Proposed Rail Demand 
Product Manifest Railcars per Day 
In Lipid Feedstock 2 
Methanol (MeOH) less than 
Out Biofuel (FAME/B100) 2 
Pitch less than 
Glycerin less than 
3.5.5. Biofuels Production Facility-Support Buildings 
A control building is proposed to be situated in the northwestern section of the proposed lease 
area (refer to Figure 3.2-1: Stockton Biofuel Production Site Plan) and would include the control 
room, an office for the production facility administrators, restroom facilities, lockers for the 
operators, control panels and control equipment, and laboratory facilities for testing to ensure 
safety and quality assurance. Other buildings at the proposed Endicott facility may include a 
utilities shed, boiler, and pipeline manifold buildings. 
The buildings would consist of a prefabricated steel metal shell designed and constructed to meet 
the requirements of the California Code of Regulations Title 24. The prefabricated buildings 
would be designed and constructed to meet the building requirements of the local, State, and 
federal agencies having jurisdiction. Pressure and humidity control would be provided where the 
environmentally sensitive electronic equipment is located or where required due to electrical area 
classification. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-32 
3.5.6. Biofuels Production Facility-Motor Control Center 
The proposed Endicott project would include a motor control center, which would be installed in 
a nonhazardous area. The motor control center would have a lighting panel to supply all 120-volt 
circuits on the site, except at the major buildings. 
3.5.7. Production Tanks (Biofuels Production Facility) and Storage Tanks (Targa 
Terminal) 
The proposed facility would include the following eight production tanks located on the Endicott 
lease area: 
. One 10,000-bbl methanol tank, 44 ft. in diameter by 40 ft. in height 
. One 7,500-bbl pitch tank, 40 ft. in diameter by 34 ft. in height 
. One 7,500-bbl glycerin tank, 40 ft.in diameter by 34 ft. in height 
. One 1,000-bbl glycerin tank, 21 ft. in diameter by 16 ft. in height 
. One 7,500-bbl effluent tank, 40 ft. in diameter by 34 ft. in height 
. One 5,000-bbl refined fatty acids tank, 30 ft. in diameter by 40 ft. in height 
. Two 5,000-bbl FAME/B100 tanks, each 30 ft. in diameter by 40 ft. in height 
Additionally, six storage tanks would be housed at the Targa facility across Navy Drive: 
. Two 25,000-bbl lipid feedstock tanks, each 67 ft. in diameter by 40 ft. in height 
. One 50,000-bbl lipid feedstock tank, 77 ft. in diameter by 60 ft. in height 
. Three 25,000-bbl FAME/B100 tanks, each 67 ft. in diameter by 40 ft. in height 
All lipid feedstock tanks, as well as the pitch, refined fatty acid, and both glycerin production 
tanks, are to be composed of 316SSL stainless steel. The balance of the tanks, FAME/B100 
storage tanks, and the methanol, FAME/B100, and effluent production tanks, are composed of 
carbon steel construction. All lipid feedstock storage tanks, the refined fatty acid tank, and the 
pitch production tank, are heated. All tanks except for the effluent production tank will be 
blanketed with a nitrogen barrier. 
The methods and emission factors for calculating fugitive emissions from equipment leaks are 
based on the EPA Protocol for Equipment Leak Emission Estimates (EPA-435-/R-95-017). For 
new Synthetic Organic Compound Manufacturing Industry (SOCMI) facilities subject to 
regulation, the typical methods for estimating fugitive leak emissions are (1) published average 
SOCMI emission factors reduced by the projected efficiencies for a Leak Detection and Repair 
Program (LDAR) or (2) the correlation equation method taking into a screening value for leak 
detection. All on site equipment will be outfitted with leak detection systems in accordance with 
applicable regulation. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-33 
3.5.7.1. Secondary Containment 
All tank areas, as well as loading and unloading areas, will have secondary containment systems 
per industry best management practices. Containment areas will be routed through in-ground 
oil/water separators. 
3.5.8. Nitrogen Production 
It is proposed that Endicott and Targa will utilize nitrogen blanketing of the lipid feedstocks and 
FAME/B100 to avoid oxidation, as oxidation is the most significant deterioration mechanism of 
these materials. Oxidation is the chemical reaction of the atmospheric oxygen, which attacks the 
fatty acid chains. In order to protect the lipid feedstock and FAME/B100 and minimize 
degradation, oxygen should not come in contact with the lipid feedstocks or FAME/B100. To 
prevent oxidation and other chemical determination/contamination (free fatty acid and 
adulteration by impurities), the general practice is to keep commodities in closed vessels in an 
atmosphere that excludes oxygen and moisture and where temperatures are controlled at 
minimum levels. Nitrogen blanketing of lipid feedstocks and FAME/B100 during storage and 
transfer from vessel to vessel will be practiced by Endicott and Targa to preserve FAME/B100. 
EndicottÕs preferred methodology of nitrogen blanketing will require a series of vessels, pressure 
controllers, and techniques to avoid vacuum conditions. The nitrogen production facility would 
house a series of air compressors, an air purification unit, chillers, heat exchangers, distillation 
column, condenser, liquid nitrogen tank, and a nitrogen vaporizer. 
3.5.9. Thermal Oxidizer 
The biofuels production facility calls for volatile organic compounds (VOCs) produced during 
the esterification process of Unit 7. VOCs such as dimethyl ether and methanol, would be 
processed with high temperature thermal oxidation to convert them the VOCs to CO2 and water. 
VOC destruction efficiency depends upon design criteria which include chamber temperature, 
residence time, inlet VOC concentration, compound type, and degree of mixing. It is expected, 
however, that the thermal oxidizer to be employed in the Endicott project will attain a 
combustion efficiency of at least 98% depending on the exact characteristics of the output vapor 
stream at any given point in the biofuel manufacturing process. 
3.5.10. Fire Protection 
The fire protection system will provide protection for the biofuel production facility, production 
tanks storage tanks, truck loading rack, railcar off-loading rack and Berth #9. A 10-inch-diameter 
fire-water system loop will be installed with hydrants and monitors spaced around the perimeter 
of the Targa tank farm as well as the biofuel production facility. The hydrants and monitors will 
be fed by the CWSC water main via a back-flow preventer. The foam system will supply foam 
solution to the production tanks, storage tanks, the truck loading rack, and the railcar off-loading 
rack. 
Storage and production tanks will be provided with either one fixed foam discharge chamber 
outlet each or with two or more outlet chambers as may be required depending on tank product 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-34 
designation. The required minimum application rate of fixed foam discharge protection for topof-
seal floating roof tanks is 0.3 gpm/ft2, and the minimum discharge time is 20 minutes. The 
foam solution piping fabrication and installation will comply with the latest edition of NFPA 
Standard 11 for low-expansion foam and combined-agent systems. 
The administration building will be equipped with an Inergen fire-suppression system. The 
Inergen fire-suppression system is an environmentally ÒgreenÓ three-dimensional firesuppression 
agent replacing Halon 1301. The systems includes critical facilities such as data 
processing rooms; telecommunications switching facilities; process control rooms; laboratory, 
and a non-water-based extinguishing agent that is electrically nonconductive, is safe for use in 
human-occupied facilities, and has zero ozone depletion and zero atmospheric lifetime. The 
system will include four discharge nozzles, heat-detection sensors, a control panel, and a 15- 
square-foot closet to house seven product cylinders. 
The emergency deluge system will consist of two combination emergency showers, eye-face 
wash units, and drench hose units located at the north side of the loading racks. The system will 
include tempered water, freeze protection, and controls. The fire-water line, fire connections, 
hydrants, valves, and pipe fittings will comply with the latest edition of NFPA Standard 24 for 
private fire service mains and their appurtenances. All fire-protection systems will be required to 
meet the requirements of the Uniform Fire Code, NFPA standards: 
¥ NFPA 30: Flammable and Combustible Liquids Code 
¥ NFPA 11: Low-, Medium- and High-expansion Foam 
¥ NFPA 13: Installation of Sprinkler Systems 
¥ NFPA 16: Installation of Foam-water Sprinkler and Foam-water Spray Systems 
¥ NFPA 24: Installation of Private Fire Service Mains and Their Appurtenances 
¥ NFPA 70: National Electrical Code 
¥ NFPA 497: Recommended Practice for the Classification of Flammable Liquids, Gases, or 
Vapors and of Hazardous (Classified) Locations for Electrical Installations in Chemical 
Process Area 
3.5.11. Lighting 
Photocell-controlled overhead lighting will be provided throughout the proposed Endicott 
Biofuel Production Facilities. Metal halide lighting is proposed for good color rendition. 
Lighting will be set at heights according to the Stockton Municipal Code and will include 
necessary hooding, shielding, and other light pollution controls to meet Stockton Municipal Code 
16.32.070 standards. 
3.5.12. Security 
Cameras will be installed for security and to monitor operations. The cameras will connect to a 
monitor and digital video recorder in the administration building. A camera will be placed 
strategically within the facility and at all entry and exit gates. All access will be controlled at 
both Targa and Endicott. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-35 
3.5.13. Access and Product Off-site Transport 
Access to the proposed biofuel production facility will be accommodated from an access gate 
entering the proposed lease area across from the access driveway for the Stockton Police Gun 
Range off of Navy Drive. This gate would allow access to facility personnel and other 
individuals who might visit the site in addition for various purposes, such as: deliveries, 
maintenance, and regulatory purposes, etc. Emergency access gates have been included in the 
site design to allow for the exit of facility personnel and emergency vehicle access in the event of 
an emergency. It is anticipated that vehicle traffic to the proposed lease area will be limited. See 
Figure 3.2-1, Stockton Biofuels Production Facility Site Plan, provides a schematic of the 
proposed access points. 
3.5.14. Emergency Shut Down System 
If required by law, the proposed Endicott project will include an emergency shutdown system. 
The system, if necessary, would consist of hard-wired push-button switches for both the transfer 
operations to the Targa Terminal and the Endicott biofuel production operations. The emergency 
shutdown system would shut down the operations by means of a permissive control system. 
3.5.15. Cathodic Protection 
The proposed biofuel production facility will utilize a system of pipelines running between the 
Targa support facilities and Endicott production facilities. These pipes will be placed both above 
and below grade; all buried piping and tank bottoms would be protected by a cathodic protection 
system. 
3.5.16. Pipeline Supply Connections 
Because the proposed biofuel production facility will take advantage of support storage and 
transfer facilities at the adjacent Targa Terminals and the Stockton Port DistrictÕs deep water 
channel Berth #9, it will be necessary to construct a network of pipelines to convey materials to 
and from the biofuel production facility, the storage terminal, and the loading/offloading 
facilities. Two pipelines will run from Berth #9 to the Targa storage facility; these lines were 
noted above in Section 3.5.2. These lines will be pumped via a manifold on the proposed 
Endicott site, and will include one carbon steel pipe for loading barges/tankers with 
FAME/B100, and another stainless steel/electric heat tracing pipe to offload lipid feedstocks. 
Additionally, there will be four additional pipelines: two carbon steel pipes running from the 
production site to Targa, carrying nitrogen, and one carrying FAME/B100 for loading trucks and 
railcars and two stainless steel pipelines, one carrying pitch, one carrying glycerin. There will 
also be a carbon steel pipe running from Targa to the biofuel production facility carrying Methyl 
Alcohol (Methanol), and another stainless steel/electric heat tracing pipe from Targa to the 
biofuel production facility carrying lipid feedstocks offloaded from truck and rail. Large 
shipments of lipid feedstocks would be delivered to the Targa storage facility via Berth #9 and 
the berth connection pipeline. The balance of the feedstock receipts would originate from railcar 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-36 
and truck shipments. See Table 3.5-10: Pipelines, for a list of dedicated pipelines. The two 
stainless steel pipelines carrying feedstocks would be outfitted with electric heat tracing, which is 
the practice of shrouding the pipe with an electrical heating element and wrapping the pipe with 
thermal insulation to keep heat from escaping). Heat tracing will be provided to keep the length 
of the pipeline at an adequate temperature to maintain free flow of the fatty acid feedstock. 
Table 3.5-10: Pipelines 
Product From To Length Pipeline Type 
Pitch Endicott 
Production 
Plant 
Targa Truck & 
Rail Racks 
833 ft. (to Targa 
manifold) 
Stainless Steel 
Glycerin Endicott 
Production 
Plant 
Targa Truck & 
Rail Racks 
833 ft. (to Targa 
manifold) 
Stainless Steel 
Fatty Acid 
Feedstock 
Targa Tank 
Storage/Truck 
& Rail Racks 
Endicott 
Production Plant 
1,531 ft. (from 
storage tanks) 
Stainless 
Steel/Electric 
Heat Tracing 
Fatty Acid 
Feedstock 
Berth #9 Targa Tank 
Storage 
6,117 ft. (to storage 
tanks) 
Stainless 
Steel/Electric 
Heat Tracing 
Biofuel 
(B100) 
Endicott 
Production 
Plant 
Targa Tank 
Storage/Truck & 
Rail Racks 
1,531 ft. (to storage 
tanks) 
Carbon Steel 
Biofuel 
(B100) 
Targa Tank 
Storage 
Berth #9 6,117 ft. (from 
storage tanks) 
Carbon Steel 
Nitrogen Endicott 
Production 
Plant 
Targa Tank 
Storage 
1,531 ft. (to storage 
tanks) 
Carbon Steel 
TOTAL 18,493 ft. 
The receiving line from the pipeline would be equipped with a metering system and connections 
for a portable prover to calibrate the meter. 
3.5.16.1. Berth #9 Pipeline Connection 
To off load lipid feedstocks from Berth #9 by barge or tanker ship, a new pipeline connection 
(roughly 6,100 feet in length) would be constructed to connect the Berth #9 facilities to the Targa 
tank storage area. This proposed pipeline would route west from Berth #9 along Port Road D, 
then south along the San Joaquin River to the proposed production facility site, then continue 
south across Navy Drive to the Targa storage facility. (See Figure 1.0-2: Biofuel Facility, 
Pipelines, Truck Rack, Rail Rack, Berth #9, and Storage Facilities Map and Figure 3.5-3 
Pipeline Route and Connection Map). 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-37 
The pipeline would accommodate a maximum flow rate of 10,000 barrels per hour (bph) and 
would be constructed of API 5L X52, WT 0.250Ó ERW pipe. The pipeline would require a fivefoot 
permanent easement and a minimum of five feet of cover above the top of the pipe within 
City of Stockton streets, and a temporary construction easement up to 50 feet in width for 
construction. 
3.5.17. Stormwater Runoff Plan 
The Port has developed a Stormwater Development Standards Plan (DSP). The project is located 
within the DSPÕs East Complex. All stormwater within this complex drains to a stormwater 
retention basin as depicted in Figure 3.4-3: Project Setting. During years when the retention 
basin reaches a high level, stormwater is pumped to the San Joaquin River (Port of Stockton 
Stormwater Development Standards Plan, Revised April 17, 2006, Page 3). The Port DSP 
specifies a number of Best Management Practice requirements that are specific to each drainage 
zone and are applicable to this project. As part of the projectÕs stormwater runoff plan, the 
proposed lease area would be subdivided into areas classified according to the means of handling 
drips, spills, and stormwater. Runoff from the project surface areas would be designed to flow to 
the PortÕs designated stormwater detention basin. The proposed Endicott project peripheral areas, 
including landscaped areas, paved walkways, and building roofs, would be drained naturally by 
percolation into the soil or by surface runoff to the stormwater collection and discharge system 
maintained by the Port. The on-site stormwater bio retention swale will also be sized to accept 
the stormwater runoff from the proposed Navy Drive widening and improvement project. 
The projectÕs stormwater runoff plan would identify contact areas as those areas where small 
quantities of product could be spilled. These may include small tanks, process- or producthandling 
equipment, or maintenance areas. These areas would be curbed or diked as required to 
contain drips or spills as well as stormwater in the amount required by the Port. After a storm 
event, the water would be tested. Tested water meeting the quality requirements would be 
discharged to the drainage-collection system. Contaminated water would be removed by vacuum 
truck or other means. 
The production facility would include plans for one stormwater bio retention basin, installed near 
the southern end of the lease area, along Navy Drive. This stormwater bio retention basin will be 
designed to remove silt and pollution from stormwater runoff, thereby filtering contaminants out 
before the water reaches the PortÕs stormwater detention basin to the south. 
3.6 Biofuel Production Facility Construction 
3.6.1. Project Construction 
Construction of the proposed project would include grading of the Endicott lease area and 
placement of foundations and infrastructure. Construction would begin with site grading, cutting, 
and filling to ensure that the lease area drained properly into the PortÕs drainage system. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-38 
Facilities that would be constructed aboveground would include the production tanks, ISBL 
production plant, control and administration building, motor control buildings, utilities building, 
thermal oxidizer, nitrogen plant, boilers, water cooling tower, and fencing. Each of these 
structures would be single story, with the esterification reactor (in the ISBL) being the tallest 
structure at 175 feet and the stack on the thermal oxidizer being between 100 and 140 feet. The 
primary materials to be used during the proposed project construction would be concrete, 
stainless steel, and carbon steel. Major process piping and production tanks would be made of 
either stainless steel or carbon steel. The major construction phases for the proposed project 
would include: 
¥ Rough grading and site staking; 
¥ Excavation and site work; 
¥ Structural facilities; 
¥ Electrical, process mechanical, and instrumentation installation; 
¥ Paving and striping; 
¥ Architectural and landscaping; and 
¥ Start up and testing. 
3.6.1.1. Rough Grading and Site Staking 
Survey staking would be used to define the limits of the proposed lease area. The lease area is 
already very flat and would require very minor grading. No tree clearing would be necessary at 
the lease area. The estimated time to complete this construction phase is two to three weeks. 
3.6.1.2. Excavation and Site Work 
Following rough grading, additional excavation would bring the lease area to final grade and 
prepare the soil for underground piping and structural slabs. The areas under the production 
tanks and ISBL would require excavation and re-compaction. For detailed discussion, please 
refer to Appendix HÑEngineering Feasibility Report). Site work would involve installing 
underground pipes (6-inch-diameter or larger), manholes, structural foundations, curbs, gutters, 
and paved areas. Excavation for concrete foundations, secondary containment wall footings, and 
underground drainage pipes would be performed with excavators and/or backhoes. This 
construction phase is expected to last four to six weeks. 
3.6.1.3. Structural Facilities 
This phase would consist of compacting and preparing the soil for all structural facilities and 
developing piers for foundation systems. Prior to pouring concrete, structural forms, rebar, and 
conduits would be installed for each facility. After the concrete is poured, it would be finished 
and cured before the forms are removed, and the overhead structural steel and roof decking 
would be erected. This construction phase is expected to last up to five months. 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-39 
3.6.1.4. Paving and Striping 
All parking areas, paved areas, and designated locations would be paved and striped. Paving 
would be performed incrementally throughout the site area as large construction and non-rubber 
tread equipment is removed from the site. This phase of construction is expected to last three to 
four weeks. 
3.6.1.5. Electrical, Process Mechanical, and Instrumentation Installation 
After the structures are erected and roofed, electrical equipment (e.g., machinery control 
consoles, switchboards, lighting, etc.) would be installed. Site work such as installing pull boxes, 
conduits, and cables would continue. Process mechanical equipment (e.g., pumps, vessel 
reactors, high pressure pumps, fat booster pumps, splitter, fatty acid flash drum, sweetwater 
pumps, evaporation surface exchanger, column feed pumps, bleachers, pre-heater, and surface 
condensers) would be installed and piped through the ISBL. Site work would continue, as smalldiameter 
chemical piping would be routed throughout the site. After roofs on buildings and 
facilities are secured, flow meters, level probes, pressure meters, and other instrumentation (e.g., 
as process analyzers) would be installed. The electrical/mechanical instrumentation construction 
phase would last from four to six months. 
3.6.1.6. Start Up and Testing 
This final phase of construction would involve Endicott personnel (i.e., operators, maintenance 
crews, and instrumentation specialists) working with equipment vendors to understand operation 
and function of equipment at the biofuel production facility. Under Endicott supervision, the 
equipment vendors would start up and test the equipment on-site to guarantee that pumps, 
gauges, and other operating equipment are functional and meet design standards. 
3.6.1.7. Berth #9 Transfer Equipment Improvements 
Transfer equipment improvements to be installed, and added at existing facilities at Berth #9 will 
include: piping, manifolds, piping hatches on berth deck, boiler, fuel stripping pumps, a vapor 
recovery system, pipeline booster pumps, electrical services, a fire water system, a foam system, 
and compressed air equipment. After ground preparation for each proposed improvement, a 
foundation and/or pad will be constructed, based on geotechnical review of the site and structural 
engineering and design calculations. Several of these improvements will be delivered in a 
Òready-to-operateÓ state from the manufacturer (such as the pumps, the boiler, and the 
compressed air system) which will require minimal connection efforts, etc. The fire water 
system will be constructed to meet necessary fire flows and local standards. 
3.6.2. Pipeline Construction 
Construction of the pipelines to support the biofuel production facility will be carried out by 
Targa Terminals, and coordinated with the Endicott construction schedule for the biofuel 
production facility. Construction of the pipeline would sequentially include right-of-way 
clearing, trenching, pipe stringing, welding, backfilling, and testing. 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-40 
3.6.2.1. Pre-construction 
The construction plan would identify specific sites for any equipment fuel storage required for 
pipeline construction. In general, equipment fuel storage sites would be located to provide 
adequate setbacks from existing water bodies (approximately l00 feet minimum) and water wells 
(approximately 200 feet minimum). Refueling of construction equipment would take place along 
the ROW using absorbent material to create temporary berms around the equipment. Prior to 
construction, Endicott would develop an Emergency Response Plan and Spill Prevention Plan, or 
similar documents, as required by law. 
3.6.2.2. Right-of-way Clearing 
The proposed construction ROW would be cleared and graded to provide for safe and efficient 
operation of construction equipment and space for temporary storage of spoil material. In 
general, the width of the ROW clearings would be kept to a practical minimum to avoid undue 
disturbance of adjacent resources. Brush clearing would be limited to trimming and/or crushing 
in those areas specified by the City or Port to avoid disturbance of root systems. Where tree 
clearing is necessary, the ROW boundaries would be flagged, and any specimen trees on the 
perimeter would be preserved from damage. Where necessary, all brush and other debris would 
be disposed of in accordance with instructions from the City, Port, or landowner, and all 
applicable laws and regulations. 
3.6.2.3. Trenching 
Typically, the installation of pipeline via conventional trenching methods would require the 
excavation of a 6- to 7-foot-deep trench to maintain a minimum of 3 to 4 feet of cover. The 
construction work area is anticipated to require a ROW up to 50 feet wide. A typical trench 
would range from 2 to 3 feet in width. The trench would be excavated using backhoes, ditching 
machines, and/or track hoes. An exception to the mechanical excavation would be hand digging 
using air tools to locate buried utilities such as other pipelines, cables, water mains, and sewers. 
No blasting is anticipated. Fugitive dust emissions at the construction site during earth-moving 
operations would be controlled as needed by water trucks equipped with spray nozzles. 
3.6.2.4. Pipe 
Pipe-stringing trucks would be used to transport the pipe in 40- to 80-foot lengths from the 
shipment point to the pipeline ROW. Trucks would carry the pipe along the ROW, and sideboom 
tractors would unload the joints of pipe from the stringing trucks and lay them end to end 
beside the ditch line for future lineup and welding. As required, coated line pipe would be bent in 
the field by a portable bending machine to fit the contour of the ditch both vertically and 
horizontally. Construction ROW conditions may require that prefabricated ÒshopÓ bends be used 
when field bending would not be practical. The pipe would be lifted and lowered into the ditch 
by an appropriate number of side-boom tractors spaced so that the weight of unsupported pipe 
would not cause damage to the pipe. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-41 
3.6.2.5. Welding and Inspection 
All field welding would be performed by qualified welders in accordance with Endicott and 
Targa specifications, including API 1104 (Standard for Welding: Pipe Lines and Related 
Facilities) and the rules and regulations of the U.S. Department of Transportation found in CFR 
Title 49 (Part 195 for liquid pipelines). One hundred percent of the welds would be 
radiographically inspected, exceeding the 10 percent inspection requirement found in CFR Title 
49, Part 195 (49 CFR Part 195). 
3.6.2.6. Backfilling 
Native material excavated from the pipeline trench would be reused for trench backfilling to the 
maximum extent possible. Where native material is not suitable for compaction, import material 
would be used in the backfilling process. Import backfill material may be soil that has adequate 
structural integrity to allow for proper compaction, sand/decomposed granite, or base rock 
material as used in road construction. 
3.6.2.7. Testing 
Hydrostatic testing would be performed after construction and before start up. Pipeline coating 
would typically be applied at a qualified coating facility before delivery to the construction site. 
However, field coating (heat-shrink polyethylene sleeves) would be necessary on all field-weld 
joints made at the site to provide a continuous coating along the pipeline. A detection test would 
be conducted to locate any coating discontinuities such as thinning or other mechanical damage 
that could permit moisture to reach the pipe. All coated pipe, including field joints, fittings, and 
bends, would be tested and repaired, as necessary, before backfilling. 
3.6.3. Project Schedule, Workforce, and Construction Hours 
Endicott anticipates construction could begin in March 2015. Construction would last for 
approximately 9 to 11 months and would be completed by the first quarter of 2016. Project 
construction would require approximately 75 temporary workers during peak construction. 
3.6.4. Construction Traffic 
Approximately 75 construction personnel would be employed during peak construction 
activities. Construction activities would occur within a 10-hour workday and would generally 
take place between the hours of 7 a.m. and 5 p.m. Temporary off-street parking for construction 
personnel would be located on adjacent property. Endicott will coordinate with the Port to utilize 
available facilities. It is not anticipated that excessively oversized loads would be required, 
except for the delivery of the tank steel and the truck loading-rack skids. An open field adjacent 
to the proposed lease area would be used for the staging of equipment such as piping, valves, and 
fittings. The staging area would be temporarily fenced (See Figure 3.6-1 Staging & Storage Area 
During Construction). Approximately two workers would be involved in loading, unloading, and 
security at the staging area, with about 8 to 10 trucks per day using this staging site during peak 
construction. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-43 
3.7 Biofuel Production Facility Operations 
3.7.1. Employment, Operating Hours, and Anticipated Traffic 
During the operational phase of the biofuel production facility Endicott plans on 20 permanent 
positions to operate and maintain the biofuel production facility. The biofuel production facility 
will operate on a 24 hour basis, 7 days per week. Endicott will run three shifts with between 4 
and 8 employees per shift. Traffic generation between shifts during a peak hour is estimated to 
be approximately 4 vehicles assuming ridesharing to the site and staggered start times. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-44 
3.8 Summary of Mitigation Measures 
Mitigation measures identified during planning for the proposed biofuel production facility and 
identified during the Initial Study Review to reduce potential significant impacts to a less than 
significant level are summarized below. 
3.8.1. Aesthetics (Visual Resources) 
None required 
3.8.2. Agriculture and Forestry Resources 
None required 
3.8.3. Air Quality 
AQ-1: Implementation of fugitive dust control measures mandated by SJVACPD Regulation 
VIII. 
AQ-2: Suspend excavation and grading activity when sustained winds exceed 20 miles per 
hour or when gusts exceed 25 miles per hour. 
AQ-3: Install wheel washers for all exiting trucks and equipment leaving the site. 
AQ-4: Use alternative fuel or catalyst-equipped diesel construction equipment. 
AQ-5: Minimize idling time (e.g., 5-minute maximum) 
AQ-6: Replace fossil-fueled equipment with electrically driven equivalents when possible. 
AQ-7: Limit or curtail construction activity during periods of high ambient pollution. 
AQ-8: Primary and Secondary Roof Seals Ð The seals prevent emissions from escaping from 
between the IFR and the tank shell. The primary seal is a metallic band (called a 
shoe) attached to the floating roof. The shoe slides in contact with the tank shell as 
the level of product in the tank rises and falls. The secondary seal is mounted above 
the primary seal. Secondary seals further reduce vapor losses from the gaps between 
the metallic shoe and tank shell. 
AQ-9: Drain Dry Design Ð A drain-dry tank can be completely drained of product using the 
standard pumping systems such that when changing between different product types 
the tank does not need to be cleaned as often. 
AQ-10: Drain Dry Vapor Recovery Unit Ð Vapors associated with the drain-dry operations 
would be extracted and condensed through a PURGIT air pollution condensers 
control system. 
AQ-11: Nitrogen Blanketing Ð Blanketing tank contents with nitrogen gas eliminates 
degradation of organic materials stored therein and acts as a buffer between tank 
contents and potential emissions. 
AQ-12: Vapor/Gas emissions from the processing of animal derived feedstocks will be 
controlled using a combination of tank & vessel transfer balancing lines, active 
carbon filtration, nitrogen blanketing and incinerated in a thermal oxidizer. 
AQ-13: All production tanks will be blanketed with nitrogen gas to prevent decomposition of 
stored materials. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-45 
3.8.4. Biological Resources 
BIO-1: Subsequent to contacting the SJCOG, a biologist retained by the SJCOG will perform 
a pre-construction survey of the site prior to any project-related ground disturbance to 
verify vegetation types affected by the project and to determine if any species covered 
by the San Joaquin County Multi-species Habitat Conservation Plan occur on the site. 
The results of the pre-construction survey will determine which Incidental Take 
Minimization Measures (if any) will be required for project approval. Incidental Take 
Minimization Measures have been established for each species covered by the Plan to 
ensure that all impacts to covered species are minimized and mitigated appropriately 
under FESA, CESA, and CEQA. 
3.8.5. Cultural Resources 
ARCH-1: In the event that unanticipated archaeological resources should be accidentally 
discovered during project construction, a qualified archaeologist or paleontologist 
will be retained for evaluation of the find. If the find is determined to be a historical 
or unique archaeological resource, appropriate mitigation or avoidance measures will 
be taken in accordance with CEQA Guidelines 15064.5(f). During mitigation of 
unanticipated archaeological resources, it would not be necessary for work to halt in 
construction areas not affected by such finds. Any historically significant cultural 
materials discovered during project construction will be the subject of professional 
scientific analysis and a report to be prepared by a qualified archaeologist. In the 
event that such a discovery should contain human remains, the following steps shall 
be taken as outlined in CEQA Guidelines 15064.5 (e)(1): 
(1) There shall be no further excavation or disturbance of the site or any nearby area 
reasonably suspected to overlie adjacent human remains until: 
(A) The coroner of the county in which the remains are discovered must be 
contacted to determine that no investigation of the cause of death is required, 
and 
(B) If the coroner determines the remains to be Native American: 
1. The coroner shall contact the Native American Heritage Commission 
within 24 hours. 
2. The Native American Heritage Commission shall identify the person or 
persons it believes to be the most likely descended from the deceased 
Native American. 
3. The most likely descendent may make recommendations to the landowner 
or the person responsible for the excavation work, for means of treating or 
disposing of, with appropriate dignity, the human remains and any 
associated grave goods as provided in Public Resources Code Section 
5097.98 or 
(2) Where the following conditions occur, the landowner or his authorized 
representative shall rebury the Native American human remains and associated 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-46 
grave goods with appropriate dignity on the property in a location not subject to 
further subsurface disturbance. 
(A) The Native American Heritage Commission is unable to identify a most likely 
descendent or the most likely descendent failed to make a recommendation 
within 24 hours after being notified by the commission. 
(B) The Descendant identified fails to make a recommendation; or 
(C) The landowner or his authorized representative rejects the recommendation of 
the descendant, and the mediation by the Native American Heritage 
Commission fails to provide measures acceptable to the landowner. 
3.8.6. Geology and Soils 
None required 
3.8.7. Greenhouse Gas Emissions 
None required 
3.8.8. Hazards and Hazardous Materials 
HM-1: Provide all employees and the Stockton Port District with a hazardous materials 
business plan that educates employees on handling and shipping of hazardous 
materials. 
HM-2: Design facilities with secondary containment for all ASTs. 
HM-3: Design all ASTs with under-tank leak detection that would meet the requirements of 
API 650. 
HM-4: Each tank foundation would have a membrane liner, which would be constructed of 
High Density Polyethylene, thereby ensuring any potential leakage is contained to the 
maximum extent possible, within the foundation area of the tank. 
HM-5: Endicott to document MSDS are made available to each employee assigned to work 
with methanol, nitrogen, glycerin, pitch, or biofuels. The MSDS should include 
specific information on the material, and should list all pertinent information 
including flashpoint, boiling point, acute and chronic effects of all chemical 
ingredients in the solution, protective equipment, as well as other fire and emergency 
cleanup information. 
HM-6: Provide the Port Fire Department with a plant/site safety plan which shall be updated 
as needed. 
HM-7: Employ leak detection (SCADA) for all pipelines to ensure that leaks are discovered, 
and all flow is shut-off, as quickly as possible. 
3.8.9. Hydrology and Water Quality 
WQ-1: Endicott and/or contractor will develop and implement an SWPPP and submit an NOI 
stating its intent to discharge stormwater to the SWRCB prior to beginning 
construction activities. The SWPPP must specify Best Management Practices that 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-47 
would minimize all construction pollutants from contacting stormwater, with the 
intent of keeping all products of erosion from moving off-site into receiving waters. 
WQ-2: Spill prevention kits shall always be in close proximity when using hazardous 
materials (e.g. crew trucks and other appropriate locations). 
WQ-3: For equipment that must be fueled on-site, containment shall be provided in such a 
manner that any accidental spill of fuel shall not be able to enter the water or 
contaminate sediments that may come in contact with water. All fueling done at the 
job site shall provide containment to the degree that any spill shall be unable to enter 
the channel or damage river and wetland vegetation. 
WQ-4: Endicott will prepare a pollutant control plan that specifies logistics and schedule for 
construction activities that will minimize the potential for erosion and standard 
practices that include monitoring and maintenance of control measures. 
3.8.10. Land Use and Planning 
None required 
3.8.11. Mineral Resources 
None required 
3.8.12. Noise 
The following mitigation measures will only be completed as required, upon receipt of noise 
related complaints resulting from the proposed project. 
NOISE-1: Installation of a silencer in the inlet air filter. 
NOISE-2: Pumps will be housed in an acoustical enclosure. 
NOISE-3: Compressors will be housed in an acoustical enclosure. 
NOISE-4: Noise barrier wall along the northern boundary will be constructed and placed to 
minimize noise off site. 
NOISE-5: Endicott will establish a telephone number for use by public to report any 
undesirable noise conditions associated with construction and operations. Telephone 
number will be posted at the project site in a manner visible to passersby. 
NOISE-6: All power equipment and vehicles associated with the project will have proper 
muffler devices. 
NOISE-7: Endicott will document, investigate, evaluate, and attempt to resolve all project 
related noise complaints. Endicott will conduct the following: Use a Noise 
Complaint Resolution Form to respond to each compliant; Attempt to contact the 
person making the noise complaint in 24 hrs.; Conduct investigation to determine 
source of noise; Reduce noise with all feasible measures upon a complaint. 
NOISE-8: Install silencer on the thermal oxidizer exhaust stack to reduce the sound emitted at 
stack exit. 
NOISE-9: Wherever feasible, erect barriers or shields near construction equipment (e.g., 
compressors, pneumatic tools, drills, generators) considered major sources of noise. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-48 
3.8.13. Population and Housing 
None required 
3.8.14. Public Services 
None required 
3.8.15. Recreation 
None required 
3.8.16. Transportation/Traffic 
TRAN-1: A traffic control plan will be developed in coordination with the City of Stockton, the 
Port, County of San Joaquin, and the California Department of Transportation District 
10. 
TRAN-2: Start times and end times of the construction day will be offset from identified peak 
traffic hours to mitigate traffic congestion on local streets and highways. 
Construction personnel will typically arrive at the project site around 6:00 AM, 
before the morning peak hour (7:00 AM to 8:00 AM). Construction employees will 
typically leave between 3:00 PM and 4:00 PM, before the evening peak hour (4:00 
PM and 5:00 PM). 
TRAN-3: The lease boundary line for the Endicott Lease has been set back at an agreed upon 
location between Endicott and the Port, to ensure all contemplated roadway 
improvements have appropriate right-of-way to accept the final 100% Design Plans. 
TRAN-4: The ingress/egress for the Endicott biofuel production facility will be located at the 
western edge of the lease area across from the Stockton Police Department Pistol 
Range. 
TRAN-5: The ingress/egress for the Endicott biofuel production facility will be a right turn only 
entrance, and a right turn only exit. 
3.8.17. Utilities and Service Systems 
UTL-1: All effluent will be pre-treated, stored in the effluent tank (7,500 bbl tank) and 
pumped to the nearby RWCF plant for treatment. 
UTL-2: The pH of the Endicott biofuel production facility effluent shall never be outside of 
the range of 5 to 9 when submitted to the RWCF system. 
UTL-3: RWCF and Endicott shall establish the expected criteria including volume, waste 
strength, discharge schedule and control strategies in conjunction with RWCF to 
ensure smooth RWCF facility operation on both sides. 
UTL-4: The stormwater retention basin will be sized to accommodate runoff from both the 
Endicott Site as well as the portion of Navy Drive from the middle of the bridge to 
the intersection at Washington Street after the realignment. 

3.0 Project Description 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 3-49 
UTL-5: Employ an approved Solid Waste Diversion and Recycling Plan. Endicott will 
develop a solid waste diversion and recycling plan in accordance with AB 341 (Solid 
Waste Diversion), which requires industrial and commercial construction efforts to 
recycle fifty percent of their industrial wastes. Such a plan would be implemented in 
conjunction with Calrecycle (formerly CIWMB) and San Joaquin County Solid 
Waste Division of the Department of Public Works (County has adopted an 
ordinance, known as Ordinance Number 4310 (2009) similar in effect to AB 341). In 
addition to the requirement of diverting commercial and construction debris, the 
County ordinance requires the Owner/Builder to complete a Diversion Report within 
30 days of completing the project. 

4.0 Environmental Factors Potentially Affected 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 4-1 
4.0 ENVIRONMENTAL FACTORS POTENTIALLY AFFECTED 
The environmental factors checked below would be potentially affected by this project, 
involving at least one impact that is a Òpotentially significant impactÓ as indicated by the 
checklist on the following pages. 
. Aesthetics . Agricultural Resources . Air Quality 
. Biological Resources . Cultural Resources . Geology/Soils 
. Green House Gas . Hazards and Hazardous 
Materials 
. Hydrology/Water Quality 
. Land Use/Planning . Mineral Resources . Noise 
. Population/Housing . Public Services . Recreation 
. Transportation/Traffic . Utilities/Service Systems . Mandatory Findings of 
Significance 
Based on the analysis presented in this IS, it has been determined that for all resource areas, the 
proposed Endicott project would not result in any significant impacts that cannot be mitigated to 
a less-than-significant level. In addition, the project may result in potentially significant impacts, 
but proposed Endicott project-specific mitigation measures would reduce the effect of such 
impacts to a level that no significant impacts would occur. On the basis of the IS and 
implementation of all proposed Endicott project-specific mitigation measures, there is no 
substantial evidence that the project as mitigated would have a significant impact on the 
environment which would trigger the necessity to prepare an EIR. The proposed MND is 
presented in Appendix A of this document. 

5.0 Determination 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 5-1 
5.0 DETERMINATION 
On the basis of the IS evaluation that follows, I find that: 
. The proposed project is exempt from CEQA pursuant to the general exemption (CEQA 
Guidelines, 15061(b)(3)), a statutory exemption, and/or a categorical exemption, and that if a 
categorical exemption, none of the exceptions to the exemption apply. A NOTICE OF 
EXEMPTION will be prepared. 
. I find that the proposed project COULD NOT have a significant effect on the environment, 
and a NEGATIVE DECLARATION will be prepared. 
. I find that although the proposed project could have a significant effect on the environment, 
there will not be a significant effect in this case because revisions in the project have been made 
by or agreed to by the project proponent. A MITIGATED NEGATIVE DECLARATION will be 
prepared. 
. I find that the proposed project MAY have a significant effect on the environment, and an 
ENVIRONMENTAL IMPACT REPORT is required. 
. I find that the proposed project MAY have a Òpotentially significant impactÓ or Òpotentially 
significant unless mitigatedÓ impact on the environment, but at least one effect 1) has been 
adequately analyzed in an earlier document pursuant to applicable legal standards, and 2) has 
been addressed by mitigation measures based on the earlier analysis as described on attached 
sheets. A TIERED ENVIRONMENTAL IMPACT REPORT is required, but it must analyze 
only the effects that remain to be addressed. 
. I find that although the proposed project could have a significant effect on the environment, 
because all potentially significant effects (a) have been analyzed adequately in an earlier EIR or 
NEGATIVE DECLARATION pursuant to applicable standards, and (b) have been avoided or 
mitigated pursuant to that earlier EIR or NEGATIVE DECLARATION, including revisions or 
mitigation measures that are imposed upon the proposed project, no further environmental 
document is required. FINDINGS consistent with this determination will be prepared.Ó 
Signature : Jason Cashman, Environmental Specialist III, Stockton 
Port District 
November 18, 2013 
Date 

6.0 Discussion of Environmental Setting, Potential Impacts, and Mitigation Measures 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-1 
6.0 DISCUSSION OF ENVIRONMENTAL SETTING, POTENTIAL 
IMPACTS, AND MITIGATION MEASURES 
The Environmental Checklist is used to assist in evaluating the potential environmental impacts 
of the proposed Endicott project. The Environmental Checklist identifies potential project effects 
as follows: 
(1) Potentially Significant Impact: An effect that is substantial based on significance 
criteria. If there are one or more Òpotentially significant impactÓ entries in the 
Environmental Checklist, an EIR is required. 
(2) Less than significant with Mitigation Incorporated: An effect that, with the 
incorporation of mitigation measures, is reduced from a Òpotentially significant impactÓ 
to a Òless than significant impact.Ó The Initial Study includes mitigation measures and 
briefly explains how these measures reduce the associated effect to a less-thansignificant 
level. 
(3) Less than Significant Impact: No significant impacts will result. 
(4) No Impact: The project will not create an impact in the category. 
Included in each discussion is a summary of relevant setting information and identified potential 
impacts and mitigation measures that apply to the proposed Endicott project. Substantiation and 
clarification for each Environmental Checklist response is also provided in the following 
resource discussions. 
CEQA provides the following guidance for evaluation of impacts: 
(1) A brief explanation is included for all answers except Òno impactÓ answers that are 
adequately supported by the background information sources a lead agency cites in the 
parentheses following each question. A Òno impactÓ answer is adequately supported if 
the referenced information sources show that the impact does not apply to the project 
(e.g., the project falls outside a fault rupture zone). A Òno impactÓ answer should be 
explained where it is based on project-specific factors as well as general standards (e.g., 
the project would not expose sensitive receptors to pollutants, based on a projectspecific 
screening analysis). 
(2) All answers must take into account the whole action involved, including off-site as well 
as on-site, cumulative as well as project-level, indirect as well as direct, and 
construction as well as operational impacts. 
(3) ÒPotentially significant impactÓ is appropriate if there is substantial evidence that an 
effect is significant. If there are one or more Òpotentially significant impactÓ entries 
when the determination is made, an EIR is required. 

6.0 Discussion of Environmental Setting, Potential Impacts, and Mitigation Measures 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-2 
(4) ÒLess than significant with mitigation incorporatedÓ applies where the incorporation of 
mitigation measures has reduced an effect from a Òpotentially significant impactÓ to a 
Òless than significant impact.Ó The lead agency must describe the mitigation measures, 
and briefly explain how they reduce the effect to a less-than-significant level. 
(5) Earlier analysis may be used where, pursuant to the tiered, program EIR, or other 
CEQA process, an effect has been adequately analyzed in an earlier EIR or Negative 
Declaration (Section 15063 (c)(3)(d)). 
(6) Lead agencies are encouraged to incorporate into the Environmental Checklist 
references to information sources for potential impacts (e.g., general plans, zoning 
ordinances). Reference to a previously prepared or outside document should, where 
appropriate, include a reference to the page or pages where the statement is 
substantiated. 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-3 
6.1 Aesthetics (Visual Resources) 
The aesthetics section addresses the potential effects of the proposed Endicott project on 
aesthetics (visual resources). This section describes existing regional visual character, visual 
resources, views of the project area from important vantage points, and the changes in these 
views that would occur with the implementation of the proposed Endicott project. 
Visual resources are the natural and cultural features of the landscape that can be seen and that 
contribute to the publicÕs appreciative enjoyment of the environment. Visual resources, or 
aesthetic impacts, are generally defined in terms of a projectÕs physical characteristics and 
potential visibility, and the extent to which the projectÕs presence would change the perceived 
visual character and quality of the environment in which it would be located. 
This section describes the visual resources setting of the project and the appearance of the 
proposed Endicott project after construction, and analyzes the potential effects of the project on 
visual resources in terms of changes to the viewshed from Key Observation Points (KOPs) near 
the project. KOPs are strategic viewing points where there are significant numbers of public 
(sensitive) viewers and from which there would be a clear view of the project after construction. 
This analysis considers the existing visual setting and its visual character and scenic quality, the 
potential sensitivity of likely project viewers to changes in the viewshed, and the visibility or 
dominance of the project after construction. 
6.1.1. Background 
6.1.1.1. Regional Setting 
The proposed project is wholly located within the Port of Stockton and is situated on a 4.91 +/- 
acre parcel of unimproved land. The Port is located within the San Joaquin Valley and is 
situated near to the San Joaquin River (and tributaries) and, as such, the Port is located on flat 
lands which do not possess significant natural topographic variation. The Port consists of 
approximately 2,000 acres of land for industrial development. The Stockton Port Commission is 
chartered to develop and operate the Port to benefit maritime uses, and it functions as a landlord 
by leasing Port properties to more than 100 tenants. In the surrounding area of the proposed 
project area the Port leases property to a variety of Port Industrial uses which are characterized 
by storage tanks, power production towers, cement and grain silos, railroad facilities, large 
storage buildings, and stockpiles of various commodities. The Port is located 75 nautical miles 
from the Golden Gate Bridge and 1 mile from Interstate 5. Local regional land uses which affect 
the visual character include: residential infill (north/northeast of the proposed project site) and 
agricultural lands (west/southwest of the proposed project area) and industrial/commercial 
facilities (south/southeast of proposed project area). 
6.1.1.2. Local Setting 
The proposed Endicott Stockton Biofuel Production Facility Project is located at the intersection 
of Navy Drive and West Washington Street in the Stockton Port District. The lease area is a 
roughly triangular in shape, and is approximately 4.91 +/- acres in size within the parcel 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-4 
identified as San Joaquin County AssessorÕs Parcel Number (APN) 145-02-007. The lease area is 
immediately adjacent to the San Joaquin River and a levee which rises above the level of the 
lease area by about 20 feet (levee is situated north of the proposed project site). Adjacent to the 
project site, are the following properties: Rough and Ready Island (also known as the PortÕs 
Western Complex) to the northwest across the San Joaquin River; the Stockton Police 
Department gun and pistol training range to the west; Pacific Ethanol production facility and 
Targa Terminals to the southwest; Yara North America terminal to the south; and, to the east, a 
rail spur and TXI-Riverside cement production facility. The entire lease area is relatively 
unimproved other than a groundwater monitoring well located near the roadway at the 
intersection of Navy Drive and West Washington Street. The terrain is primarily flat throughout 
the entire lease area with a very slight slope to the west/southwest toward Navy Drive. The entire 
property sits below the level of the levee which runs along the San Joaquin River along the 
northern edge of the property and the elevated portion of Navy Drive to the west which climbs to 
the height of the levee at the northern end of the property. See Figure 3.4-3: Project Setting, 
shows the surrounding land uses. 
6.1.1.3. Regulatory Context 
Federal Regulations 
No federal regulations apply to the proposed Endicott projectÕs visual resource issues. 
State Regulations 
California Scenic Highway Program 
CaliforniaÕs Scenic Highway Program was created by the Legislature in 1963 to preserve and 
protect scenic highway corridors from change that would diminish the aesthetic value of lands 
adjacent to highways. The State laws governing the Scenic Highway Program are found in the 
Streets and Highways Code Section 260, et seq. The State Scenic Highway System includes a list 
of highways that are either eligible for designation as scenic highways or have been so 
designated. These highways are identified in Section 263 of the Streets and Highways Code. A 
list of CaliforniaÕs scenic highways and a map showing their locations may be obtained from the 
California Department of TransportationÕs Scenic Highway Coordinators. There are no 
designated State scenic highways in the immediate vicinity of the proposed Endicott project. 
Local Regulations 
City of Stockton 2035 General Plan 
The Stockton 2035 General Plan sets out policies for land use, circulation, community facilities, 
and environmental resource management for the City. It includes a chapter, Community Design, 
which specifically addresses urban design issues. Discussions under the Community Design 
chapter which may be applicable to the proposed project are as follows: 
Community Design (CD) 
CD-1 To improve the overall visual quality of the urban environment. 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-5 
CD-1.1 Urban Design Plans 
The City shall ensure that plans for districts, corridors and villages reflect citywide urban design 
concepts set out in the General Plan. 
CD-1.2 Contrast Between Urban and Rural 
The citywide design framework shall heighten the contrast between rural, natural, and urban 
areas as one enters and travels through the community. 
CD-1.3 Travel Experience 
To the extent possible, the City shall ensure that all public and private investments in StocktonÕs 
districts and villages contribute positively to the overall travel experience by automobile, rail, 
pedestrian and bicycle in the community. 
CD-1.4 Transition to Rural Landscapes 
Transitions between urban and rural areas at the edge of the community shall not diminish the 
visual quality of open space. Soundwalls and utilitarian edges of developments shall not be 
allowed as an interface between development and rural landscapes. 
CD-1.5 Gateways 
The City shall define a set of distinctive gateway districts that provide a sense of arrival. 
Gateway districts shall use a combination of streetscape, building orientation and placement, and 
signage to create memorable community entries. 
CD-1.6 Open Space Features 
The City shall promote community design that incorporates the open space features of 
StocktonÕs waterways, wetlands, and parks into the travel experience. This includes visual access 
to open space features and private and public investment that visually frames and complements 
natural landscapes and parks. 
CD-1.7 Rail Corridors 
The City shall work with transportation agency partners and private property owners to improve 
maintenance, code enforcement, screening, and landscaping of view sheds along rail transit 
corridors in Stockton. 
CD-1.8 Highway 99 Beautification 
The City shall work with Caltrans and private property owners to improve the visual quality of 
traveling on Highway 99 in Stockton by improving the maintenance of the highway ROW and 
adjacent properties, code enforcement, reducing the number of billboards, encouraging new 
investment on visible sites, landscaping, and screening industrial uses. 
6.1.1.4. Required Permits and Approvals 
No visual resource permits are required for the proposed Endicott project. 
6.1.2. Methodology 
A qualitative assessment of the existing and future visual environment within the project area 
was conducted to determine whether there would be significant impacts resulting from the 
construction of the Endicott project. Visual elements of the proposed Endicott project were 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-6 
evaluated in relation to the existing visual character in the vicinity of the project. Potential KOPs 
were reviewed within the project area and viewer sensitivities were identified. 
6.1.2.1. Viewer Sensitivity 
Visual perception is the basic act of seeing or recognizing an object. Physical conditions that 
affect perception and ability to discern details are: (1) observer distance and (2) speed. As 
observer distance increases, the ability to see the details of an object decreases. As observer 
speed increases, the sharpness of lateral vision decreases and the observer tends to focus along 
the line of travel. Vehicle passengers are able to focus on the passing landscape for longer 
periods than the driver. Viewer groups are differentiated by the physical factors that modify 
perception. 
6.1.2.2. Viewer Response 
Changes to the visual environment are subjectively evaluated by the affected viewers. To 
understand and predict viewer response to the changes resulting from project construction, it is 
necessary to make assumptions about the viewers who may see the project and the aspects of the 
visual environment to which they are likely to respond. Table 6.1-1: Viewshed Ratings, below 
explains viewshed ratings and descriptions. 
Table 6.1-1: Viewshed Ratings 
Rating Description 
Outstanding 
Visual Quality 
A rating reserved for landscapes with exceptionally high visual quality. These landscapes will 
be significant regionally and/or nationally. They usually contain exceptional natural or cultural 
features that contribute to this rating. They will be what we think of as Òpicture postcardÓ 
landscapes. People will be attracted to these landscapes to be able to view them. 
High Visual 
Quality 
Landscapes that have high quality scenic value. This may be due to cultural or natural features 
contained in the landscape or to the arrangement of spaces contained in the landscape that 
causes the landscape to be visually interesting or a particularly pleasing place for people. These 
are often landscapes which have high potential for recreational activities or in which the visual 
experience is important. 
Moderately High 
Visual Quality 
Landscapes which have above average scenic value but are not high scenic value. The scenic 
value of these landscapes may be due to manmade or natural features contained within the 
landscape, to the arrangement of spaces in the landscape, or the two dimensional attributes of 
the landscape. 
Moderate Visual 
Quality 
Landscapes which have average scenic value. They usually lack significant manmade or natural 
features. Their scenic value is primarily a result of the arrangement of spaces contained in the 
landscape and the two dimensional visual attributes of the landscape. 
Moderately Low 
Visual Quality 
Landscapes that have below average scenic value but not low scenic value. They may contain 
visually discordant manmade alterations but the landscape is not dominated by these features. 
They often lack spaces that people would perceive as inviting and provide little interest in terms 
of two dimensional visual attributes of the landscape. 
Low Visual 
Quality 
Landscapes with low scenic value. These landscapes are often dominated by visually discordant 
manmade alterations or they are landscapes that do not include spaces that people will find 
inviting and lack interest in terms of two dimensional visual attributes. 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-7 
6.1.3. Environmental Setting 
6.1.3.1. Regional Overview 
The City of Stockton is located in a historic floodplain adjacent to the San Joaquin River. The 
major natural visual characteristics of the area include a flat topography and scattered sloughs, 
creeks, rivers, levees, and riparian vegetation located along the various waterways. Distant views 
of the coastal mountain ranges (including Mount Diablo) are available throughout the region. 
The proposed Endicott project is located within the Delta region of California, which is very flat 
with numerous levees that limit sight distance in the area. Due to the industrial developed nature 
of the area, minimal topographic relief, and lack of natural vegetative features, the existing land 
uses are the strongest determining factor for visual character. The dominant visual features of the 
area are industrial facilities and warehousing structures. The Interstate 5 bridge structure over the 
Delta at the eastern end of the Port area provides the highest point within the region to view the 
Port and the proposed project area for the biodiesel production facility. This freeway overpass is 
located approximately 2 miles east of the proposed project lease area. 
Industrial, residential, and recreational facilities, including the Stockton Country Club, Louis 
Park and the Rivera Cliffs area are located to the north of the Port across the Stockton Deep 
Water Shipping Channel (DWSC). Residential areas north of the DWSC are primarily across 
from Docks 14 and 20 which are not associated with or located near to the proposed project. 
Additional residential areas east of the Port are near Washington Street and southwest of the I-5 
interchange for Navy Drive and are also not visible from the proposed project area. Other 
industrial, agricultural, and residential areas are located south and east of the Port. 
Because this portion of the City is so highly developed with industrial and port infrastructure, 
few, if any, natural features exist within the area. Open space near the proposed project area 
exists along the levee of the San Joaquin River. The relative visibility of the proposed project 
area from residences, industrial, institutional, and commercial properties is low. The vantage 
points with the clearest views of the proposed project area are distant elevated locations such as 
from the overpass on Interstate 5. Furthermore, the general viewshed is highly disrupted by 
existing man made industrial or commercial infrastructure, ranging from the Interstate 5 overpass 
structure, to infrastructure at the Port (above ground storage tanks, Pacific Ethanol grain 
elevators, TXI cement silos, marine loading arms at Berth #10, conveyance structures, train 
tracks, levees, undeveloped parcels of land, etc.). The minimal topographic relief does not 
provide the viewers with a vivid viewshed. As a result of the existing development, the viewer 
sensitivity remains low to moderately low for commercial and industrial viewers, and moderate 
to more distant residential viewers. As such, these viewers, who are already in an impacted 
viewshed, will receive minimal, if any, impact from the proposed project. 
6.1.3.2. Potential Project Visibility 
Identification of the projectÕs viewshed was based on review of project engineering drawings, 
visual simulations of the projectÕs appearance from a birdÕs-eye view, study of topographic maps 
and air photos, and extensive field observations (See Figure 6.1-1: Site Elevation Plan). The 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-8 
viewshed map indicates two categories of view areas: (1) those in which the proposed project 
area would likely be generally visible; and (2) those in which views toward the proposed project 
area and its ancillary facilities would likely be blocked for the most part, but may be visible from 
specific locations. The boundaries of the viewshed were set to the south sides of the proposed 
lease area along the San Joaquin River levee, where views were not otherwise blocked by the 
raised rail spur, buildings, trees, or other obstructions. This distance was selected because 
elements of a view that are beyond the levee distance are considered part of the backgroundÑthe 
landscape zone in which little color or texture is apparent, colors blur into values of blue or gray, 
and individual visual impacts become least apparent (USDA Forest Service 1973, pp. 56-57). 
The proposed Endicott project facilities would be most visible in views immediately adjacent to 
the project and from a short portion of the San Joaquin River levee. In most cases, views of the 
project features beyond the immediate vicinity would be completely blocked by intervening 
structures, and natural features of the area. 
6.1.3.3. Sensitive Viewing Areas 
Views of the proposed project area are limited due to flat terrain, vegetative growth, and 
surrounding industrial development. Unobstructed views of the proposed project area are limited 
to locations immediately adjacent to the proposed project area. The area surrounding the 
proposed project area is dominated by various industrial and institutional facilities including 
cement production facilities, petroleum terminals, a gun range, existing biomass power plant, and 
other heavy industry. The nearest sensitive viewers with potential to experience a visual impact 
from the proposed project are residents in neighborhoods situated .6-.8 miles from the project, 
drivers/passengers on Navy Drive/West Washington Street, and participants in recreational 
activities along the San Joaquin River. For the purpose of determining potential visual impacts to 
sensitive receptors in the project vicinity, the following four Key Observation Points (KOPs) 
were identified: 
KOP 1 Ð Navy Drive/West Washington Street: All views from KOP 1 are dominated by the 
heavy industrial facilities in the immediate vicinity of the project area extending through the 
middle ground into the background. Sensitive viewers are likely to have the most substantial 
(defined as duration of view and predominance of the proposed Endicott infrastructure) at the 
intersection of Navy Drive and West Washington Street. Motorists and pedestrians (there is little 
to no foot traffic in this area) at this intersection would have unobstructed views of the project 
for limited (likely less than 15 seconds) lengths of time while stopped at the intersection. 
Sensitive viewers traveling northbound on Navy Drive would have the longest and most direct 
view of the project (likely duration of 20-30 seconds). From this perspective the facilities of the 
adjacent TXI-Riverside cement plant are also plainly visible in the foreground including a rail 
spur, silos, and administrative buildings; in the middle ground, beyond the rail spur, a rusty 
storage tank, and a large mound of sulfur (bright yellow color) are plainly visible as well as large 
marine loading arms and cranes rising above the San Joaquin river; the towers of a high tension 
power transmission line protrude from the background. Additionally, any viewer arriving at this 
intersection would have extended, unobstructed views of the tank farm facilities located 
immediately south of the project featuring dozens of white above ground storage tanks of 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-9 
different shapes and sizes, and various terminalling and storage equipment including pumps, 
pipelines, etc. The Pacific Ethanol production facility would also be visible by the viewer to the 
southwest. A variety of port facilities are clearly visible in the middle ground to the east, and 
include: cranes, water towers, silos, tanks, warehouses, overhead power lines etc. Due to the 
nature of the existing fore and middle ground of this viewshed, the proposed Endicott project is 
consistent with the visual nature of existing facilities (bulk, shape, color, texture, etc.) in the area 
and would not represent a significant impact to any potential viewer and no mitigation measures 
will be required for KOP 1 viewers. (See Figure 6.1-2: Endicott Project KOPs Views) 
KOP 2 Ð San Joaquin River: The San Joaquin River is a public waterway which extends from 
the south-central Sierra Nevada mountain range to its confluence with the Sacramento River at 
Suisun Bay. This section of the river is generally utilized for commercial shipping as well as 
recreational (limited) purposes. A stretch of the river which runs parallel to the project; visual 
impacts to viewshed may include impacts to sensitive viewers. The surface of the project area is 
not visible from KOP 2 as the San Joaquin River levee obscures its view. However, structures 
adjacent to the project site including buildings and silos at TXI-Riverside, overhead power lines, 
and Yara North America storage tanks, as well as other structures can be seen rising above the 
levee in the middle ground and background. It is therefore likely that the structures (operations 
and maintenance buildings, cooling towers, etc.) associated with the proposed Endicott project 
would be visible to sensitive viewers. However, such structures would not represent a significant 
impact as all proposed structures would be consistent with existing development in size, shape, 
color, and bulk, visible within the fore and middle ground. The proposed Endicott structures are 
consisted with the existing viewshed, and would not further degrade the aesthetic value of the 
KOP 2 viewshed. (See Figure 6.1-2: Endicott Project KOPs Views) 
KOP 3 Ð Boggs Tract: Boggs Tract is an older neighborhood consisting of roughly 100 acres 
and is isolated from other Stockton residential areas by Interstate 5, The San Joaquin River, The 
Port of Stockton, and industrial/commercial facilities along Highway 4. The view toward the 
project area from KOP 3 is dominated by unimproved vacant lots in the immediate foreground 
along with a discordant mix of weathered and new commercial buildings. The middle ground 
consists of many large white above ground storage tanks at the Westway Terminal, silver colored 
Port water towers, utility poles, and many power lines. The background viewshed is disrupted by 
a large blue building and tall yellow and gray smokestack/column. The site of the proposed 
Endicott project is an additional .4 miles beyond the farthest visible structure from KOP 3 with 
industrial facilities completely obscuring the view of the project area. It is extremely unlikely 
that any aspect of the proposed project will be visible from any point of Boggs Tract, including 
any proposed vertical structures. All proposed columns or tanks would be constructed in a 
manner consistent with the existing structures that is visible in the middle and foregrounds. As 
such, visual quality of the viewshed from KOP 3 and would not be impaired, and therefore, 
would not represent a significant impact to sensitive receptors in the Boggs Tract neighborhood. 
(See Figure 6.1-2: Endicott Project KOPs Views) 
KOP 4 Ð Louis Park: Louis Park is a fairly large recreation area located approximately .78 
miles northwest of and across the San Joaquin River from the proposed project site. This park is 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-10 
an open space that features baseball, basketball, and tennis facilities and is the closest park to the 
proposed project area. The area in and around the park is dominated by tall trees. The view 
from KOP 4 toward the proposed project area consists of the park in the foreground which 
includes a view a mix of trees and park structures, including: tower lightings, baseball fencing, 
grandstands, and an equipment/maintenance shed. The background is completely dominated by 
trees, and includes a few telephone poles. No Port infrastructure was viewed from KOP 4 as 
potential views of these structures were obstructed by the trees and telephone poles. It is 
unlikely that the proposed Endicott infrastructure would be visible from this KOP; however, if it 
were visible from KOP 4, such structures would be consistent with the other large manmade 
structures (telephone poles and lighting) and would not impact the aesthetic value of KOP 4. See 
Figure 6.1-2: Endicott Project KOPs Views. 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-12 
Figure 6.1-2: Endicott Project KOPs Views 
Locations of KOP 1 through 4 
KOP 3 Ð Boggs Tract Ð Westward view from the intersection 
of W. Washington Street and S. Ventura Ave. Various 
Industrial facilities visible in middle ground and background. 
KOP 4 Ð Louis Park Ð View to the South East from Louis Park. 
Distance, geography, and intervening vegetation obscure 
views in the direction of the proposed project site. 
KOP 2 - San Joaquin River Ð Southeastern view from across the 
San Joaquin River toward the proposed project site. TXIRiverside 
and YARA facilities are visible 
KOP 1 - Navy Drive/West Washington Street Ð View towards the 
northeast across Navy Drive. TXI-Riverside facilities visible beyond 
the proposed Endicott project area. 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-13 
6.1.4. Standards of Significance 
An impact to aesthetics would be considered significant if the project would: 
¥ Prove to be inconsistent with the goals and policies of the Stockton General Plan 2035 and 
the Port of StocktonÕs West Complex Plan; 
¥ Have a substantial adverse effect on a scenic vista; 
¥ Substantially damage a major landform or scenic resources, including, but not limited to, 
trees, rock outcroppings, and historic buildings within a State scenic highway; 
¥ Substantially degrade the existing visual character or quality of the site and its surroundings; 
or 
¥ Create a new source of substantial light or glare, which would adversely affect day or 
nighttime views in the area. 
6.1.5. Impacts and Mitigation Measures 
No significant impacts to aesthetics or visual resources were identified as a result of the proposed 
Endicott project. As a result, project-specific mitigation measures to reduce visual impacts are 
not required. 
6.1.6. Aesthetics Initial Study Responses 
Table 6.1-1: Aesthetics Initial Study Responses 
WOULD THE PROJECT: 
Potentially 
Significant 
Impact 
Less Than 
Significant 
Impact with 
Mitigation 
Incorporated 
Less Than 
Significant 
Impact 
No 
Impact 
a) Have a substantial adverse effect on 
a scenic vista? 
. . . . 
b) Substantially damage scenic 
resources, including, but not limited 
to, trees, rock outcroppings, and 
historic buildings within a state scenic 
highway? 
. . . . 
c) Substantially degrade the existing 
visual character or quality of the site 
and its surroundings? 
. . . . 
d) Create a new source of substantial 
light or glare that would adversely 
affect day or nighttime views in the 
area. 
. . . . 

6.1Aesthetics 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-14 
6.1.7. Responses to Initial Study Questions 
6.1.7.1. Scenic Vistas: No Impact 
The proposed Endicott project would not interfere with any scenic vistas or damage any scenic 
resources. The existing visual character in the vicinity of the proposed project area is not 
considered scenic, and, therefore, there would be No Impact to scenic vistas. 
6.1.7.2. Damages to Scenic Resources: No Impact 
The proposed Endicott project would not damage scenic resources, including, but not limited to, 
trees, rock outcroppings, and historic buildings within a State scenic highway. The proposed 
project area has no trees, rock outcroppings, historic structures, or other scenic resources. Due to 
the fact that the existing visual character of the vicinity of the proposed lease area is not 
considered scenic, there will thus be a less-than-significant impact to scenic vistas or scenic 
resources. 
6.1.7.3. Visual Character: No Impact 
The proposed lease area is currently vacant and the existing visual character will not be changed 
by the proposed Endicott project. The proposed Endicott project calls for improvements with 
similar scale, density, and building materials as existing industrial development surrounding the 
proposed project area. There is no State scenic highway near to or affected by the proposed 
Endicott project. The existing visual character of the proposed project area is not considered 
scenic; therefore, there would be No Impact. 
6.1.7.4. Light and Glare: Less than Significant 
The proposed Endicott project would include parking lot and security lighting. The nearest 
sensitive receptor is located approximately 0.6 miles from the proposed project area, across the 
San Joaquin River. The industrial land uses adjacent to the proposed project area are existing 
sources of light and glare. A significant increase in light or glare in the area would not be 
occasioned by this project. All lighting for the proposed Endicott project would be designed so 
that it does not adversely impact adjacent areas. Exterior lighting will be designed with shields 
and light directed only onto the biofuel production facility, ISBL unit, and production tanks. 
Only lighting that is absolutely necessary for safety and operation purposes will remain on at 
night. Therefore, the impact is considered less than significant. 

6.2 Agriculture 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-15 
6.2 Agriculture and Forestry Resources 
This section describes the proposed project as it could affect agricultural and forestry conditions 
and describes applicable federal, state, and local farmland conservation policies. 
6.2.1. Background 
6.2.1.1. Regulatory Context 
California Department of ConservationÕs Farmland Mapping and Monitoring Program Lands 
The Farmland Mapping and Monitoring Program (FMMP) was designed by the Soil 
Conservation Service in 1982 as a non-regulatory system that categorizes important farmland 
through the State of California. The goal of the program is to provide maps and data to various 
stakeholders to assist them in making land planning decisions with regard to the best utilization 
of CaliforniaÕs farmlands. The important farmland categories are Prime Farmland, Farmland of 
Statewide Importance, Unique Farmland, and Farmland of Local Importance. 
Williamson Act Farmlands 
The California Land Conservation Act of 1965, commonly referred to as the Williamson Act, 
enables local governments to enter into contracts with private landowners for the purpose of 
restricting specific parcels of land to agricultural or related open space use. In return, landowners 
receive property tax assessments that are much lower than normal because they are based upon 
farming and open space uses as opposed to full market value. 
6.2.2. Methodology 
Information related to agricultural resources and zoning was obtained from California 
Department of Conservation maps, and City of Stockton 2035 General Plan and Zoning District 
maps. Site inspection of the proposed project area confirmed the existing conditions of the area 
and the surrounding land uses. 
6.2.3. Environmental Setting 
6.2.3.1. Regional Overview 
The Port lies on the banks of the San Joaquin River about 40 miles south of the Port of West 
Sacramento and about 60 miles east of the Port of San Francisco in central California. The Port 
consists of approximately 2,000 acres of existing industrial uses related to shipping and receiving 
of goods and commodities. The Port and related industrial land uses are planned for in regional 
and community plans. The proposed project area is centrally located within the port and 
industrial planned area and does not abut agricultural property or designated Williamson act 
contracted land. 

6.2 Agriculture 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-16 
6.2.3.2. Study Area Setting 
The City of Stockton 2035 General Plan designates the proposed project area for industrial use, 
and the zoning classification is Port District (PT). The proposed project has never supported 
agricultural production. The proposed project has never supported forestry resources. The land 
within the Port area has been subdivided to small industrial parcels, which are not conducive to 
agricultural production. All property surrounding the proposed project area has been developed 
for industrial and port land uses and no agricultural production occurs within the area. The 
proposed project area is zoned for non-agricultural uses, which precludes the lease area from 
qualifying for Williamson Act contracts. 
6.2.4. Standards of Significance 
An impact to agriculture would be considered significant if the project would: 
¥ convert Prime Farmland, Unique Farmland, or Farmland of Statewide Importance 
(Farmland), as shown on the maps prepared pursuant to the Farmland Mapping and 
Monitoring Program of the California Resources Agency, to non-agricultural use; 
¥ conflict with existing zoning for agricultural use or a Williamson Act contract; and/or 
¥ involve other changes in the existing environment that, due to their location or nature, could 
result in conversion of Farmland to non-agricultural use. 
6.2.5. Impacts and Mitigation Measures 
The construction and operation of the proposed Endicott project would not require the 
conversion of prime agricultural land to non-agricultural uses nor would it affect timberlands. 
The proposed project area is situated in an area that has been designated as an area deemed 
acceptable for industrial land uses such as the proposed Endicott project. The proposed project 
area is not within a Williamson Act contract for agricultural land preservation. Furthermore, 
there are no existing forest lands within the Port that would be affected by the construction of the 
proposed Endicott project. Developing the proposed Endicott project at this location would 
make optimal use of the existing infrastructure and public services of the City and the Port while 
conserving prime agricultural lands and timberlands. 

6.2 Agriculture 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-17 
6.2.6. Agriculture and Forestry Initial Study Responses 
Table 6.2-1: Agriculture and Forestry Initial Study Responses 
WOULD THE PROJECT: 
Potentially 
Significant 
Impact 
Less Than 
Significant 
Impact with 
Mitigation 
Incorporated 
Less Than 
Significant 
Impact 
No 
Impact 
AGRICULTURAL RESOURCES: In determining 
whether impacts to agricultural resources are 
significant environmental effects, lead agencies 
may refer to the California Agricultural Land 
Evaluation and Site Assessment Model (1997) 
prepared by the California Department of 
Conservation as an optional model to use in 
assessing impacts on agriculture and farmland. 
Would the project: 
a) Convert Prime Farmland, Unique Farmland, 
or Farmland of Statewide Importance 
(Farmland), as shown on the maps 
prepared pursuant to the Farmland Mapping 
and Monitoring Program of the California 
Resources Agency, to non-agricultural use? 
. . . . 
b) Conflict with existing zoning for agricultural 
use, or a Williamson Act contract? 
. . . . 
c) Conflict with existing zoning for, or cause 
rezoning of, forest land (as defined in Public 
Resources Code section 12220(g)), 
timberland (as defined by Public Resources 
Code section 4526), or timberland zoned 
Timberland Production (as defined by 
Government Code section 51104(g))? 
. . . . 
d) Result in the Loss of forest land or 
conversion of forest land to non-forest use? 
. . . . 
e) Involve other changes in the existing 
environment which, due to their location or 
nature, could result in conversion of 
Farmland to non-agricultural use or 
conversion of forest land to non-forest use? 
. . . . 

6.2 Agriculture 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-18 
6.2.7. Responses to Initial Study Questions 
6.2.7.1. Convert Designated Farmland: No Impact 
There would not be any changes in the existing environment that could result in the conversion 
of Prime Farmland, Unique Farmland, or Farmland of Statewide Importance to non-agricultural 
use. The proposed Endicott project would not convert farmland as none exists in the project area. 
Therefore, there would be No Impact. 
6.2.7.2. Zoning Conflict and Williamson Act Contract: No Impact 
The proposed Endicott project is zoned as PT and is not subject to a Williamson Act contract. 
Therefore, there would be No Impact. 
6.2.7.3. Conflict with Existing Forest Land, Timberland, or Timberland Production 
Zones: No Impact 
The proposed Endicott project would not involve other changes in the existing environment that, 
due to their location or nature, could result in conversion of forest land, timberland, or 
timberland zoned Timberland Production. The spatial relationship of the proposed project area 
relative to any such land is such that the two land uses would not conflict. The nearest forest 
area is over 50 miles from the proposed project area, and the nearest timberland would be no 
closer as there are no timberland zoned properties within San Joaquin County as of 2001 
(CDFFP 2002 confirmed by CDFFP 2010). The proposed Endicott project would therefore not 
involve other changes in the existing environment that could result in conversion of timberland 
or forest land. Therefore, there would be No Impact. 
6.2.7.4. Result in the Loss of Forest Land: No Impact 
The proposed Endicott project is zoned as PT and possesses no forestlands. Furthermore, the 
nearest forest resources are located in the Stanislaus Forest which is well over 50 miles from the 
proposed project area. Therefore, there would be No Impact. 
Involve Changes that Could Result in 1.1.1.5 Conversion of Farmland or Forestland 
As discussed above, throughout this section there is no existing forest or farm land in the nearby 
vicinity of the proposed project area that could be converted. Therefore, there would be No 
Impact. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-19 
6.3 Air Quality 
This section describes the impacts of the proposed Endicott project on local and regional air 
quality. The two primary sources of odor and air contaminants from the proposed project consist 
of construction-related emissions and operational emissions, i.e., particulate matter (fugitive 
dust) from surface disturbance activities, such as grading preparation, and other short-term 
emissions from fuel combustion in equipment, including semi-trucks, graders, trenchers, pavers, 
backhoes, and front-end loaders. Dust and fumes from increased traffic associated with 
construction can also reduce air quality. The presence of contaminants does not equate to an 
environmental or health risk unless minimum threshold values are exceeded. Air contaminants 
released from construction and operational activities may include: gases, particulate matter 
(dust), gases in diesel exhaust such as nitrous oxide, nitrogen dioxide, formaldehyde, benzene, 
sulfur dioxide, hydrogen sulfide, carbon dioxide, and carbon monoxide can also create health 
problems. 
6.3.1. Background 
6.3.1.1. Regulatory Context 
Federal Regulations 
The United States Environmental Protection Agency (EPA) is responsible for enforcing the 
many federal environmental and hazardous waste laws. California is under the jurisdiction of 
EPA Region IX, with offices in San Francisco. The federal Clean Air Act of 1970 (CAA), last 
amended in 1990, authorized the establishment of national health-based air quality standards, set 
deadlines for their attainment, and established actions required of areas in the nation that 
exceeded these standards. Under the CAA, state and local agencies in areas that exceed the 
National Ambient Air Quality Standards (NAAQS) are required to develop state implementation 
plans (SIP) to show how they will achieve the NAAQS. The EPAÕs responsibility to control air 
pollution in individual states is primarily to review submittals of SIPs that are prepared by each 
state. 
The following federal regulations and standards would apply to the proposed Endicott project: 
Title V (40 CFR Part 70) 
This regulation establishes the minimum standards for State permit programs. This requirement 
comes from Title V of the CAA, as amended in 1990. Implementation of the Title V program is 
delegated to the San Joaquin Valley Air Pollution Control District (SJVAPCD), and addressed in 
District Rule 2520. Major sources are those that have actual or permitted potential emissions in 
excess of specific thresholds depending on the attainment status of the SJVAPCD. They are 
identified in tons per year for any of the following: nitrogen oxide (NOx), volatile organic 
compounds (VOCs), sulfur oxides (SOx), carbon monoxide (CO), and PM10. Title V also 
identifies major sources as those that emit 10 tons per year of any single hazardous air pollutant 
(HAP), or 25 tons per year of any combination of HAPs. Sources subject to Title V would be 
required to submit the Title V application to the SJVAPCD within 12 months of commencing 
operations. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-20 
Title IV (40 CFR Parts 72 Ð 80) 
The acid rain provisions of the CAA as amended in 1990 are implemented by the SJVAPCD via 
Rule 2540. The proposed Endicott project would be subject to Rule 2540 and would be required 
to hold sulfur dioxide (SO2) allowances to cover all SO2 emissions on an annual basis. The 
proposed Endicott project would have to file a Title IV application with the SJVAPCD and EPA 
and enter into the SO2 allowance tracking system. 
New Source Performance Standards (40 CFR Part 60 Subparts 60.1-60.5250) 
District Rule 4001 incorporates these federal standards. 
National Ambient Air Quality Standards 
The EPA has set NAAQS for several air pollutants on the basis of human health and welfare 
criteria. Two types of NAAQS have been established: primary standards, which protect public 
health; and secondary standards, which protect the public welfare from non-health-related 
adverse effects such as visibility reduction. Primary NAAQS were established for the following 
several ÒcriteriaÓ air pollutants listed in Table 6.3-1. 
Table 6.3-1: National Ambient Air Quality Standards 
Air Pollutant Averaging 
Time 
Units1 NAAQS Attainment Status 
Ozone 8-hour 
1-hour 
ppm 
ppm 
0.075 
------ 
Nonattainment/Severe 
Carbon monoxide 8-hour 
1-hour 
ppm
ppm 
9 
35 
Attainment 
Attainment 
Nitrogen dioxide Annual 
average 
1-hour 
ppm 
ppm 
0.053 
0.1 
Attainment 
Sulfur dioxide Annual 
average 
24-hour 
1-hour 
ppm 
ppm 
ppm 
0.5 
0.075 
------ 
Attainment 
Fine particulate matter 
(PM2.5) 
Annual 
average 
24-hour 
.g/m3.g/m3 12 
35 
Nonattainment 
Respirable particulate 
matter (PM10) 
Annual 
24-hour 
.g/m3.g/m3 ------- 
150 
Attainment 
Lead 3 month 
average 
.g/m3 
0.15 
No Designation 
1ppm = parts per million; .g/m3 = microgram per cubic meter 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-22 
State Regulations 
In California, the California Air Resources Board (CARB) is responsible for preparing and 
enforcing the federally required SIP in an effort to achieve and maintain NAAQS and California 
Ambient Air Quality Standards (CAAQS), which were developed as part of the California Clean 
Air Act (CCAA) adopted in 1988. CAAQS for criteria pollutants are equal to or more stringent 
than NAAQS, and include other pollutants for which there are no NAAQS. In addition, CARB is 
responsible for assigning air basin attainment and nonattainment designations in California. Air 
basins are designated as being in attainment if the levels of a criteria air pollutant meet the 
CAAQS for the pollutant, and are designated as being in nonattainment if the level of a criteria 
air pollutant is higher than the CAAQS. 
CARB is the agency responsible for regulating statewide air quality, but implementation and 
administration of CAAQS is delegated to 35 regional air pollution control districts (APCD) and 
air quality management districts (See Figure 6.3-1 California Air Basins Map). These districts 
have been created for specific air basins, and have principal responsibility for: 
¥ developing plans to meet CAAQS and NAAQS; 
¥ developing control measures for non-vehicular sources of air pollution necessary to achieve 
and maintain CAAQS and NAAQS; 
¥ implementing permit programs established for the construction, modification, and operation 
of air pollution sources; 
¥ enforcing air pollution statutes and regulations governing non-vehicular sources; and, 
¥ developing employer-based trip-reduction programs. 
To regulate air pollutant emissions within California, the state has been divided into 15 air basins 
based upon similar meteorological and geographic conditions and consideration for political 
boundary lines whenever practicable. The proposed Endicott project is located in the San Joaquin 
Valley Air Basin (Air Basin), which is the second largest air basin in California and is defined by 
the Sierra Nevada to the east, the Coast Ranges to the west, and the Tehachapi Mountains to the 
south (See Figure 3.3-1). This Air Basin includes San Joaquin County, Merced County, Madera 
County, Fresno County, Kings County, Tulare County, and a portion of Kern County. 
The proposed project would be subject to CARBÕs air quality rule making. 
Assembly Bill (AB) 2588 Air Toxics Hot Spots Program 
The proposed Endicott project may be required to prepare and submit an air toxics emission 
inventory plan and report pursuant to a time frame and schedule set by the SJVAPCD. Data 
derived from the air toxics report would then be used to score the facility with respect to ÒriskÓ 
issues. Since a screening health risk assessment would be part of the initial permitting submittal, 
the need for a specific AB 2588 risk assessment would be determined at this time by the 
SJVAPCD. Air toxics reports are periodically updated. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-23 
California Ambient Air Quality Standards 
States may establish their own standards, provided the state standards are at least as stringent as 
the NAAQS. California has established CAAQS pursuant to California Health and Safety Code 
(CHSC) [¤39606(b)] and its predecessor statutes. The CAAQS are provided in Table 6.3-2. The 
CHSC [¤39608] requires CARB to identify and classify each air basin in the state on a pollutantby-
pollutant basis. Subsequently, CARB designated areas in California as nonattainment based 
on violations of the CAAQSs. 
Table 6.3-2: California Ambient Air Quality Standards 
Air Pollutant 
Averaging 
Time 
Units CAAQS Attainment Status 
Air Pollutant 
Averaging 
Time 
Units CAAQS Attainment Status 
Ozone 
8-hour 
1-hour 
ppm 
ppm 
0.07 
0.09 
Nonattainment 
Nonattainment/Severe 
Carbon monoxide 
8-hour 
1-hour 
ppm 
ppm 
9 
20 
Attainment/Unclassified 
Nitrogen dioxide 
Annual 
average 
1-hour 
ppm 
ppm 
0.03 
0.18 
Attainment 
Sulfur dioxide 
Annual 
average 
24-hour 
1-hour 
ppm 
ppm 
ppm 
------- 
0.04 
0.25 
Attainment 
Respirable particulate matter 
(PM10) 
Annual 
average 
24-hour 
.g/m3 
.g/m3 
20 
50 
Nonattainment 
Fine particulate matter (PM 2.5) 
Annual 
average 
24-hour 
.g/m3 
.g/m3 
12 
------ 
Nonattainment 
Sulfates 24-hour .g/m3 25 Attainment 
Lead (Pb) 
30-day 
average 
.g/m3 
1.5 
Attainment 
Visibility-reducing particulates 
(VSP) 
8-hour ------- 
see 
notea 
Unclassified 
Note: In sufficient amount to produce an extinction coefficient of 0.23 per kilometer due to particles when the 
relative humidity is less than 70 percent 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
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Local Regulations 
The SJVAPCD was formed in 1992 and is the lead air quality regulatory agency for the San 
Joaquin Valley Air Basin. The SJVAPCD has jurisdiction over all point and area sources except 
mobile sources (such as motor vehicles), consumer products, and pesticides. In addition to 
planning responsibilities, the SJVAPCD possesses permitting authority over stationary sources. 
The SJVAPCD and CARB have joint responsibility for attaining and maintaining the NAAQS 
and CAAQS in the Air Basin. 
The SJVAPCD is a CEQA Responsible Agency for the proposed Endicott project via the 
SJVAPCD Permits Required Rule (Rule 2010) and New Source Review Rule (Rule 2201). 
In 2006, the SJVAPCD implemented the Indirect Source Review (ISR) rule, which requires 
developers of larger residential, commercial, and industrial projects to reduce smog-forming and 
particulate emissions generated by their projects. In general, new development contributes to the 
air-pollution problem in the San Joaquin Valley (Valley) by increasing the number of vehicles 
and vehicle miles traveled. In 2005, on-road vehicles generated approximately 200 tons per day 
of nitrogen oxides (NOx) and direct respirable particulate matter (PM10) pollution in the Valley. 
Although new, cleaner technology is reducing per-vehicle pollution, these reductions are offset 
by the emissions increase from increased traffic due to new developments. ISR applies to 
development projects that have yet to gain discretionary approval. Pursuant to the SJVAPCD 
regulations, the proposed Endicott project would not be subject to ISR, although it will be 
subject to Rule 2201. 
As part of their jurisdictional responsibilities, the SJVAPCD and CARB operate ambient air 
quality monitoring stations in numerous locations within the district boundaries. These stations 
provide real-time air quality data to the public, identify times when air quality could have 
adverse health effects to those exposed, and to determine attainment status with federal and State 
air quality standards. The three closest monitoring stations are provided in Table 6.3-3. 
The Port is under the jurisdiction of the SJVAPCD and has adopted a set of local air regulations 
that would apply to the permitting, construction, and operation of the proposed Endicott project. 
New Source Review 
The SJVAPCD New Source Review rule (Rule 2201) requires the following: 
¥ No net increase in emissions above specified thresholds from new and modified stationary 
sources for all nonattainment pollutants and their precursors 
¥ Determination of Best Available Control Technology (BACT) 
¥ Emissions impact analysis on ambient air quality 
¥ Prevention of significant deterioration increments, Class 1 areas, etc. 
¥ Analysis of threshold applicability 
Ð Major source classification thresholds (see Table 6.3-4) 
Ð Emissions offset threshold levels (see Table 6.3-5) (threshold of CO in attainment areas 
can possibly be increased if certain conditions are met) 
¥ Comply with public notice and hearing requirements 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-25 
Table 6.3-3: Ambient Air Monitoring Sites near the Proposed Endicott project 
Site Name AIRS Agency Address 
Pollutants 
Monitored1 
Approximate 
Distance from 
Site 
Stockton- 
Hazelton 
60771002 CARB 1593 E 
Hazelton 
Street, 
Stockton, CA 
95205 
O3, PM10, 
PM2.5, CO, 
NO2, TAC 
3.5 miles 
Stockton- 
Wagner-Holt 
School 
60773010 SJVAPCD 8778 Brattle 
PI, Stockton, 
CA 95209 
PM10 9.0 miles 
Tracy Airport 60773005 SJVAPCD 5749 S. Tracy 
Boulevard, 
Tracy, CA 
95376 
O3, PM10, 
PM2.5, NO2 
20.0 miles 
1O3 = ozone; PM10 = respirable particulate matter; PM2.5 = fine particles; CO = carbon monoxide; NO2 = nitrogen 
dioxide; TAC = toxic air contaminants 
Table 6.3-4: Major Source Emission Thresholds 
Pollutant Major Source Threshold (pounds/year) 
Reactive organic gases 20,000 
Nitrogen oxides 20,000 
Carbon monoxide 200,000 
Fine particles 200,000 
Respirable particulate matter 140,000 
Sulfur oxides 140,000 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-26 
Table 6.3-5: Emission Offset Threshold Levels 
Pollutant 
Stationary Source Potential to Emit 
(pounds/year) 
Reactive organic gases 20,000 
Nitrogen oxides 20,000 
Carbon monoxide (nonattainment areas) 30,000 
Carbon monoxide (attainment areas) 200,000 
Sulfur oxides 54,750 
Respirable particulate matter 29,200 
SJVAPCD General Prohibitory Rules 
The listed rules are the primary prohibitory rules that may apply to the proposed Endicott project. 
The list is of potential regulations to the project not limited to these regulations and may include 
additional rules as details of the proposed project are developed. 
Rule 4001 implements the general provisions of the StateÕs nuisance requirements and 
prohibition on circumvention. 
Rule 4002 adopts 40 CFR 60(C) national emissions standards for hazardous air 
pollutants. 
Rule 4101 prohibits the emission of visible air contaminants to the atmosphere. 
Rule 4102 states that no entity shall emit contaminants or other materials which cause 
injury, detriment, nuisance or annoyance to any considerable number of persons or to the 
public. 
Rule 4104 stipulates that gas/vapor effluent from equipment used in the reduction of 
animal matter shall be incinerated. 
Rule 4201 establishes an emission standard for particulate matter at 0.1 grain per cubic 
foot of exhaust gas. 
Rule 4202 establishes an emission standard for particulate matter as ratio of emissions to 
process weight rate. 
Rule 4301 limits emissions of combustion contaminants, sulfur compounds and NO2 
produced from the burning of fuel. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
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Rule 4304 provides an equipment tuning procedure for boilers, steam generators and 
process heaters to control visible emissions and emissions of both nitrogen oxides (NOx) 
and carbon monoxide (CO) 
Rules 4305, 4306, and 4320 limit emission of oxides of nitrogen (NOx) and carbon 
monoxide (CO), and other materials from boilers, steam generators, and process heaters. 
Rule 4311 limits the emissions of volatile organic compounds (VOC), oxides of nitrogen 
(NOx), and sulfur oxides (SOx) from the incineration of vapor emissions. 
Rule 4351 establishes that emissions from boilers, steam generators, and process heaters 
will be consistent with levels of reasonably available control technology (RACT). 
Rule 4623 and 4624 limit volatile organic compound (VOC) emissions from the storage 
and transfer of organic liquids. 
Rule 4691 limits VOC emissions from vegetable oil processing operations and to provide 
the administrative requirements for recording and measuring emissions. 
Rule 4701 and Rule 4702 limit the emission of NOx, CO, and reactive organic gases 
(ROG) from internal combustion engines. 
Rules 8011, 8021, and 8041 limit the emission of fugitive PM10 and implement the visual 
emissions standards, which are 20 percent opacity. 
Rule 8061 establishes control measures and design criteria to limit fugitive dust emissions 
from paved and unpaved Roads. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
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SJVAPCD Thresholds of Significance 
The SJVAPCD recommended thresholds for determining whether projects have significant 
adverse air quality impacts are provided in its Guide for Assessing and Mitigating Air Quality 
Impacts 2002 Revision (GAMAQI). These thresholds are provided in Table 6.3-6. 
Table 6.3-6: SJVAPCD Control District Thresholds of Significance 
Pollutant Threshold of Significance 
Reactive organic gases 10 tons/year 
Nitrogen oxides 10 tons/year 
PM10, Respirable particulate 
matter 
N/A, See Regulation VIII 
PM2.5 Fine particulate matter N/A, See Regulation VIII 
Carbon monoxide 9 parts per million (ppm) (8-hour average) 
20 ppm (1-hour average) 
Toxic air contaminants Probability of contracting cancer for the Maximally Exposed 
Individual (MEI) exceeds 10 in one million. 
Ground-level concentrations of non-carcinogenic toxic air 
contaminants would result in a Hazard Index greater than 1 
for the MEI. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
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Required Permits and Approvals 
The SJVAPCD would require an Authority to Construct and Permit to Operate for stationary 
emission sources at the proposed biofuel production facility. 
CARB would require Motor Vehicle Fuel Distribution Certification. 
6.3.2. Methodology 
Emissions from the proposed Endicott project construction and operations were estimated using 
appropriate methodology provided by the SJVAPCD, CARB, and EPA. Mobile source, 
stationary source, and fugitive tank emissions were modeled using the following software: 
California Emissions Estimator Model (CalEEMod), EPAÕs SCREEN3 MODEL, and EPA 
TANKS 4.0.9d software. To determine whether the calculated emissions and the impacts to air 
quality are significant environmental effects, CEQA guidelines have been addressed. 
Methanol emissions for the proposed Endicott facility can be approximated by using a 
scaling/proportioning factor. A prior permitted biofuel facility listed methanol emissions 
(calculated by LFR in 2006/7) of a 5 million gallon per year American Biodiesel, Inc. facility in 
Stockton as 2.5 ton/year (see table 6.3-7 below). The proposed Endicott facility would produce 
approximately 60 million gallons of biodiesel per year. The Endicott facility throughput is 
approximately 12 times larger, emissions of methanol would therefore be expected to be about 
12 times higher (30 tons/year) for a traditional facility of equivalent size to the proposed Endicott 
facility. 
Table 6.3-7: Traditional Biodiesel Methanol Emissions 
Pollutant Reactor 
Process 
Line 
Settling 
Process 
Line 
Neutralization 
Process Line 
Biodiesel 
Flash 
Unit 
Glycerol 
Flash 
Unit 
Fugitive 
Emissions 
Total 
Emissi 
ons 
tons/year tons/year tons/year tons/year tons/year tons/year tons/year 
Methanol 0.02 0.12 0.01 0.91 1.37 0.19 2.5 
Because EndicottÕs patented technology for the production of fatty acid methyl esters has not 
previously been employed on an industrial level, air quality modeling for operational emissions 
have been performed using conservative assumptions based on the traditional transesterification 
production process. However, it is assumed that final emissions values from the proposed 
Endicott facility will be drastically lower than those represented here as pilot studies have 
determined EndicottÕs esterification process to emit markedly less volatile organic compounds, 
such as methanol, than traditional facilities. Operational emissions sources include production 
tanks, employee vehicle traffic, and ISBL production facilities. Emissions from these sources are 
summed and compared to thresholds of significance. Mitigation measures are recommended 
where necessary. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
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6.3.3. Environmental Setting 
Air quality is an important factor in the health and the quality of life of a community. Air 
pollutants have the potential to adversely affect human health, wildlife, climate, visibility, and 
agriculture. In recent years, awareness of the global effect of air quality has increased and as a 
result the regulatory frameworkÕs efforts to limit air pollutant emissions have intensified, 
particularly in California. 
6.3.3.1. Regional Overview 
The climate within the SJVAPCD is typical of inland valleys in California, with hot, dry 
summers and cool, mild winters. Daytime temperatures in the summer often exceed 100 degrees, 
with lows in the 60s. In winter, daytime temperatures are usually in the 50s, with lows around 35 
degrees. Radiation (Tule) fog is common in the winter, and may persist for days. Winds are 
predominantly up-valley (from the north) in all seasons, but more so in the summer and spring 
months. Winds in the fall and winter are generally lighter and more variable in direction, but 
generally blow toward the south and southeast. 
Because of the ValleyÕs unique physical characteristics, its pollution potential is very high. 
Surrounding elevated terrain, in conjunction with temperature inversions, frequently restrict 
lateral and vertical dilution of pollutants. Ozone, the major component of the ValleyÕs 
summertime smog, is formed via chemical reactions between hydrocarbons and nitrogen oxides 
(NOx) in the presence of ultra-violet radiation or sunlight. Abundant sunshine and warm 
temperatures in summer are ideal conditions for the formation of photochemical oxidants, and 
the Valley becomes a frequent scene of photochemical pollution (ozone). 
Tiny particles of solids or liquids (excluding pure water) that are suspended in the atmosphere 
are known as Particulate matter (PM) and are classified according to their diameter in microns as 
either PM2.5 or PM10. Particulate matter can be emitted directly (primary PM, such as dust or 
soot), and can form in the atmosphere through photochemical reactions or gaseous precursors 
(secondary PM). Much of the ValleyÕs ambient PM10 and PM2.5 is secondary PM, formed in 
atmospheric reactions of NOx. 
6.3.3.2. Air Quality Pollutants 
Ozone 
Ozone is the most prevalent of a class of photochemical oxidants formed in the urban 
atmosphere. O3 is formed via chemical reactions between volatile organic compounds (VOCs are 
referred to as ROGs throughout) and nitrogen oxides in the presence of ultra-violet radiation or 
sunlight. Unlike other criteria pollutants, O3 is not emitted directly into the atmosphere by any 
sources; it is only formed when the precursor compounds are present. These precursor 
compounds (reactive hydrocarbons and NO2) are generated by combustion sources such as 
factories and automobiles as well as evaporation of solvents and fuels. The health effects of O3 
are eye irritation and deterioration of lung tissues. O3 can damage materials such as rubber, and 
also harm plants, crops, and marine life. O3 concentrations in the SJVAPCD are some of the 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-31 
highest in the country, with the highest concentrations during summer when sunlight is most 
abundant. 
Carbon Monoxide 
Carbon monoxide is a colorless, odorless gas emitted from combustion processes. Nationally 
and, particularly in urban areas, the majority of CO emissions to ambient air come from mobile 
sources. CO can cause harmful health effects by reducing oxygen delivery to the bodyÕs organs 
and tissues. At extremely high levels, CO can cause death. 
Currently, air quality meets the current ambient air quality CO standards throughout the country. 
Most sites have measured concentrations below the national standards since the early 1990s, 
since which time improvements in motor vehicle emissions controls have contributed to 
significant reductions in ambient concentrations. 
Particulate Matter 
Particulate matter consists of solid and liquid particles of dust, soot, aerosols, and other matter 
that are small enough to remain suspended in the air for a long period of time. Particulate matter 
is regulated in two categories based upon diameter. Course particles (PM10) are between 2.5 and 
10 microns in diameter and arise primarily from natural processes such as wind-blown dust. 
PM2.5 are fine particles less than 2.5 microns in diameter and are produced mostly from 
combustion or burning. Fine particles typically have more adverse health effects, because they 
are small enough to absorb into the lung tissue. Particulate matter in the air is from both natural 
sources (wind-blown dust and pollen) and manmade sources (combustion, automobiles, field 
burning, factories, and road dust). A portion of the particulate matter in the atmosphere is also a 
result of photochemical processes. The effects of high concentrations on humans include 
aggravation of chronic diseases, including heart/lung disease. 
Greenhouse Gases 
Greenhouse gases are heat-trapping compounds that absorb and emit radiation within the thermal 
infrared range. This process is the fundamental cause of the greenhouse effect, which results in 
global climate change. The primary GHGs in the EarthÕs atmosphere include water vapor, carbon 
dioxide (CO2), methane, nitrous oxide, O3, and fluorinated gases (hydrofluorocarbons and 
perfluorocarbons). The primary sources of these GHG are as follows: 
Carbon Dioxide 
Carbon dioxide enters the atmosphere through the burning of fossil fuels (oil, natural gas, and 
coal), solid waste, trees and wood products, and also as a result of other chemical reactions (e.g., 
manufacture of cement). CO2 is also removed from the atmosphere (sequestered) when it is 
absorbed by plants as part of the biological carbon cycle. 
Methane 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-32 
Methane is emitted during the production and transport of coal, natural gas, and oil. Methane 
emissions also result from livestock and other agricultural practices and by the decay of organic 
waste in municipal solid waste landfills. 
Nitrous Oxide 
Nitrous oxide is emitted during agricultural and industrial activities, as well as during 
combustion of fossil fuels and solid waste. 
Fluorinated Gases 
Hydrofluorocarbons (HCFCs), perfluorocarbons, and sulfur hexafluoride are synthetic, powerful 
greenhouse gases that are emitted from a variety of industrial processes. Fluorinated gases are 
sometimes used as substitutes for ozone-depleting substances (i.e., chlorofluorocarbons, HCFCs, 
and halons). These gases are typically emitted in smaller quantities, but because they are potent 
GHGs, they are sometimes referred to as High Global Warming Potential gases. 
Ozone 
See above definition of Ozone. 
Reactive Organic Gases 
ROGs are photochemically reactive gases that play a role in ozone formation. This definition 
excludes methane, CO, CO2, carbonic acid, metallic carbides or carbonates, ammonium 
carbonates, methylene chloride, methyl chloroform and various chlorofluorocarbons, but 
includes VOCs. VOCs are a group of carbon-containing compounds that evaporate readily at 
room temperature. Examples of VOCs include trichloroethane; trichloroethylene; and benzene, 
toluene, ethylbenzene, and xylene. These contaminants typically are generated from metal 
degreasing, printed circuit board cleaning, gasoline, and wood-preserving processes. 
VOCs can cause, eye, nose, and throat irritation; headaches, loss of coordination, nausea; and 
damage to the liver, kidney, and central nervous system. Some organics can cause cancer in 
animals; some are suspected or known to cause cancer in humans. Key signs or symptoms 
associated with exposure to VOCs include conjunctival irritation, nose and throat discomfort, 
headache, allergic skin reaction, dyspnea, declines in serum cholinesterase levels, nausea, 
emesis, epistaxis, fatigue, and dizziness. 
The ability of organic chemicals to cause health effects varies greatly from those that are highly 
toxic to those with no known health effect. As with other pollutants, the extent and nature of the 
health effect depends on many factors, including level of exposure and length of time exposed. 
Eye and respiratory tract irritation, headaches, dizziness, visual disorders, and memory 
impairment are among the immediate symptoms that some people have experienced soon after 
exposure to some organics. 

6.3 Air Quality 
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Sulfur Oxides 
Sulfur oxides refer to a group of highly reactive gasses that includes, SO, SO2, SO3 SnO, S7O2, 
and S6O2. Among these gasses, SO2 is the most common and typically used as an indicator for 
SOx. The largest sources of SO2 emissions are from fossil fuel combustion at power plants (73 
percent) and other industrial facilities (20 percent). Smaller sources of SO2 emissions include 
industrial processes such as extracting metal from ore, and the burning of high-sulfur-containing 
fuels by locomotives, large ships, and non-road equipment. SO2 is linked with a number of 
adverse effects on the respiratory system. 
Current scientific evidence links short-term exposures to SO2, ranging from 5 minutes to 24 
hours, with an array of adverse respiratory affects, including bronchoconstriction and increased 
asthma symptoms. These effects are particularly important for asthmatics at elevated ventilation 
rates (e.g., while exercising or playing). 
Studies also show a connection between short-term exposure and increased visits to emergency 
departments and hospital admissions for respiratory illnesses, particularly in at-risk populations 
such as children, the elderly, and asthmatics. 
Nitrogen Oxides 
The sum of nitric oxide and nitrogen dioxide is commonly called nitrogen oxides. Other oxides 
of nitrogen, including nitrous acid and nitric acid are part of the nitrogen oxide family. While the 
EPAÕs NAAQS covers this entire family, NO2 is the component of greatest interest and the 
indicator for the larger group of nitrogen oxides. NO2 forms quickly from emissions from cars, 
trucks, and buses; power plants; and off-road equipment. In addition to contributing to the 
formation of ground-level ozone and fine particle pollution, NO2 is linked with a number of 
adverse effects on the respiratory system. 
NOx reacts with ammonia, moisture, and other compounds to form small particles. These small 
particles penetrate deeply into sensitive parts of the lungs and can cause or worsen respiratory 
disease such as emphysema and bronchitis, and can aggravate existing heart disease, leading to 
increased hospital admissions and premature death. 
6.3.3.3. Hazardous Air Pollutants 
Hazardous Air Pollutants (HAPs) are air contaminants that are known or suspected to cause 
acute, chronic, or carcinogenic effects to human health. They are known in some sources as 
TACs. According to the EPA Technology Transfer Network Air Toxics Web Site, almost 200 
HAPs have been identified. The sources of HAPs are mostly of human origin, including 
refineries, automobiles, gasoline stations, and painting operations. 
6.3.4. Standards of Significance 
An impact to air quality would be considered significant if the proposed project would: 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-34 
¥ Conflict with or obstruct implementation of the applicable air quality plan; 
¥ Violate any air quality standards or contributes substantially to an existing or projected air 
quality violation; 
¥ Result in a cumulatively considerable net increase of any criteria pollutant for which the 
project region is in nonattainment under an applicable federal or state ambient air quality 
standard (including releasing emissions that exceed quantitative thresholds for ozone 
precursors); 
¥ Expose sensitive receptors to substantial pollutant concentrations; and/or 
¥ Create objectionable odors affecting a substantial number of people. 
To determine whether a project has the potential to obstruct implementation of the applicable air 
quality plans, contribute to potential air quality violations, or result in a cumulatively 
considerable net increase of a criteria pollutant for which the Air Basin is nonattainment, the 
SJVAPCD has established thresholds of significance for construction impacts, project 
operations, and cumulative impacts. For construction impacts, the pollutant of greatest concern 
to the SJVAPCD is PM10. The SJVAPCD recommends that significance be based on a 
consideration of the control measures to be implemented during project construction. According 
to the SJVAPCD, compliance with Regulation VIII and implementation of appropriate 
mitigation measures to control PM10 emissions are considered to be sufficient to render a 
projectÕs construction-related impacts less than significant (GAMAQI, 2002). 
The SJVAPCDÕs Guide for Assessing and Mitigating Air Quality Impacts (GAMAQI) also 
includes significance criteria for evaluating operational-phase emissions from direct and indirect 
sources associated with a project. Indirect sources include those covered under permit with the 
SJVAPCD. For this analysis, the proposed Endicott project would be considered to have a 
significant effect on the environment if it would: 
¥ Cause a net increase in pollutant emissions of ROG or NOx exceeding 10 tons per year, 
¥ Cause a violation of state CO concentration standards (The level of significance of CO 
emissions from mobile sources is determined by modeling the ambient concentration under 
project conditions and comparing the resultant 1- and 8-hour concentrations to the respective 
State CO standards of 20.0 and 9.0 parts per million.), 
¥ Frequently expose members of the public to objectionable odors, and/or 
¥ Expose the public to project-related toxic air contaminants in excess of the following 
thresholds: 
Ð probability of contracting cancer for the Maximally Exposed Individual exceeds 10 in 
one million, 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-35 
Ð ground-level concentrations of non-carcinogenic TACs would result in a Hazard Index 
greater than 1. 
Lastly, any project that would individually have a significant air quality impact would also be 
considered to have a significant cumulative air quality impact. Impacts of local pollutants are 
cumulatively significant when modeling shows that the combined emissions from the project and 
other existing and planned projects in the area would exceed air quality standards. 
6.3.5. Impacts and Mitigation Measures 
This section details potential Air Quality impacts that might arise from the construction and 
operation of the proposed Endicott project and the mitigation measures to be implemented in 
association with said impacts. 
6.3.5.1. Construction Impacts 
Construction of the proposed Endicott project is anticipated to begin around March 2015 and is 
expected to last a period of 9 to 11 months. The construction phases consist of final grading and 
site staking; excavation and site work; trenching; building of structural facilities; installing 
electrical, process mechanical, and instrumentation equipment; paving and striping; and finally 
architectural coating. 
The emissions for the construction of the proposed Endicott project at the Port of Stockton were 
estimated CalEEMod 2013.2.2. Information concerning project construction has been taken from 
Endicott prototype facility designs as outlined in the project description. The relevant 
construction specifications and assumptions for use in CalEEMod are provided in Tables 6.3-8 
and 6.3-9. 
The construction-related emissions estimates and SJVAPCD thresholds of significance are 
provided in Table 6.3-9. The data output files generated by CalEEMod are provided in Appendix 
E. 
Table 6.3-8: General Construction Assumptions 
Specifications Assumptions 
Site area (acres) 4.9 
Construction start date March 1, 2015 
Construction duration 11 months 
Hours per day 10 
Days per week 5 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-36 
Table 6.3-9: Phase-specific Construction Assumptions 
According to the SJVAPCDÕs Guidelines for Assessing and Mitigating Air Quality Impacts 
(GAMAQI), the thresholds of significance for construction-related ozone precursors (NOx and 
ROG) are calculated on a yearly basis and should not exceed 10 tons/year. CalEEMod estimates 
for the proposed Endicott projectÕs construction-related NOx and ROG fall well below these 
thresholds resulting in a less than significant impact. 
Fugitive particulate matter emissions (PM10) are the greatest pollutant of concern for a projectÕs 
construction emissions (GAMAQI, 2002). The PM10 emissions in tons/year have been quantified 
using CalEEMod. However, there is no quantified threshold provided by the SJVAPCD. The 
GAMAQI, rather, states that PM10 emissions are hard to predict and can vary greatly depending 
on several changing variables such as weather conditions, soil conditions, and the specific 
activity taking place. To address the temporary issue of fugitive dust emissions from the 
proposed Endicott projectÕs construction activity, the SJVAPCD mandates compliance with 
Regulation VIII. The mitigation measures outlined in Regulation VIII shall be adhered to during 
the construction of the proposed project reducing all PM10 impacts to less than significant 
levels. 
CalEEMod 
Phase Name 
Dates Description Equipment Used 
Worker 
Trips 
Rough Grading 
and Site 
Staking 
3/2/15 - 
3/30/15 
Site Preparation Default CalEEMod Equipment Default 
Excavation and 
Site Work 
3/31/15 
- 
5/12/15 
Grading Default CalEEMod Equipment Default 
Structural 
Facilities 
5/13/15 
Ð 
10/13/15 
Building 
Construction 
Default CalEEMod Equipment 75/day 
Paving 
10/14/15 
Ð 
11/11/15 
Paving Default CalEEMod Equipment Default 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-37 
Table 6.3-10: Construction Emissions Estimates 
Pollutant 
CalEEMod Estimate 
(tons/year) 
Thresholds of Significance 
Reactive organic gases 0.1491 10 tons/year 
Nitrogen oxides 1.2718 10 tons/year 
Respirable particulate 
matter (PM10) 
0.1338 N/A 
See Regulation VIII 
Particulate matter (PM2.5) 0.0954 N/A 
See Regulation VIII 
Carbon monoxide .9916 9 ppm 
Incorporating Regulation VIII into the mitigation measures ensures that NOx, ROG and PM 
emissions would be fully in compliance with applicable thresholds, resulting in a less-thansignificant 
impact. CO emissions are less than significant because the applicable source, 
vehicular emissions, is not substantial according to the SJVAPCD guidelines. 
6.3.5.2. Operations Impacts 
The operational emissions were evaluated for the proposed Endicott project at projected 2016 
operating capacity. Operational emissions sources include the ISBL production line, a natural gas 
fired boiler, production tanks, and employee vehicle traffic. Emissions from the four sources are 
considered in relation to applicable regulations and thresholds of significance and used to 
address CEQA guidelines. Mitigation measures are recommended where necessary. 
Operational emissions for the ISBL portion of the proposed Endicott biofuel production facility 
were modeled based on industry standard emissions rates for traditional biodiesel facilities. This 
method was used to make conservative determinations about baseline emissions levels of the 
proposed Endicott biofuel production facility despite anticipation that the implementation of 
EndicottÕs patented technology would result in substantially lower environmental impacts as 
compared to the traditional biodiesel production technology. A screening level modeling analysis 
using EPAÕs SCREEN3 MODEL was conducted with an emission rate for routine operation of 
2.15 g/s and conservative input parameters (Model data included in Appendix E). The 
concentration of methanol at the nearest sensitive receptor location (~calculated at 0.65 miles 
away) was found to be approximately 58.09 micrograms per cubic meter (ug/m3). This coincides 
with a chronic hazard index of 0.0145 and acute hazard index of 0.0021. The chronic and acute 
hazard indexes must be below 1 to avoid TBACT requirements and CEQA HAPs thresholds of 
significance. Even when using very conservative modeling parameters, they are well below the 
thresholds and therefore represent no significant impact. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-38 
Table 6.3-11: Boiler Emissions Estimates 
Boiler Emissions 
Pollutant Tons/year Lb/hr 
Nox 3.5082 0.88 
CO 9.2090 2.30 
PM (total) 0.8331 0.21 
VOC .6030 0.15 
Along with the ISBL facilities, the principle stationary emissions source at the proposed Endicott 
biofuel production facility will be a natural gas fired boiler. In keeping with other equipment to 
be operated at the proposed biofuel production facility, the boiler would conform to the 
SJVAPCDÕs CCAP by implementing BPS including the equipping of low NOx burners and flue 
gas recirculation. Implementation of said BPS measures ensures that all emissions fall below 
thresholds established by state, local, and federal policy (see table 6.3-11: Boiler Emissions 
Estimates, detailed model data can be found in Appendix E). 
6.3.5.3. Production Tank Impacts 
Table 6.3-12: Production Tanks 
Tank # Material Size (BBLS) 
Throughput 
(Barrels/Year) 
1 
B100 
(FAME) 
5,000 952,621.50 
2 
B100 
(FAME) 
5,000 952,621.50 
3 Pitch 7,500 117,397.20 
4 Glycerin 7,500 135,555.90 
5 Glycerin 1,000 18,065.90 
6 Effluent 7,500 133,465.30 
7 RFA 5,000 1,755,432.20 
8 Methanol 10,000 243,357.30 
Production tank emissions are the result of leaks and transfer losses that occur during the 
operation of the tanks. The emissions were estimated using the EPA TANKS 4.0.9d software, 
which utilizes equations developed by the API. The output files from the TANKS software is 
provided in Appendix F along with detailed calculation spreadsheets. The proposed Endicott 
project will feature eight production tanks at the biofuel production facility (see table 6.3-12 
Production Tanks). However, the bulk of these tanks will contain materials with no potential to 
release VOCs. Methanol is the only material to be stored at the proposed Endicott biofuel 
production facility with potential to release VOCs; therefore, only emissions from the methanol 
tank have been subjected to modeling (see table 6.3-13 Methanol Tank Emissions). 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-39 
Table 6.3-13: Methanol Tank Emissions 
Annual Losses (tons) 
Tank 
Contents 
Rim Seal 
Loss 
Withdrawal 
Loss 
Deck Fitting 
Loss 
Deck Seam 
Loss 
Total 
Emissions 
Methyl 
Alcohol 
0.032 2.59 0.079 0.00 2.70 
All tanks will feature nitrogen blanketing which acts as a buffer between tank contents and the 
atmosphere. Although nitrogen blanketing severely limits the possibility of VOC emissions, tank 
modeling has been performed, per EPA guidance, without accounting for this measure. This 
method of modeling allows for a conservative estimate of worst case scenario emissions from 
tanks considered. Notwithstanding the rigor of the modeling performed as compared to the 
equipment to be installed, all emissions values are well within the thresholds allowed by local, 
state, and federal regulations and therefore represent a less than significant impact. 
6.3.5.4. Employee Vehicle Traffic Impacts 
The emissions associated with employees commuting to and from work were computed using 
CalEEMod emissions modeling software. 
The proposed Endicott project is estimated to employ 20 permanent personnel at full operational 
level. For the purpose of traffic emissions modeling, it has been assumed that these 20 
employees will access the Endicott site split over three shifts and that a certain portion of said 
employees would participate in ride sharing. The assumptions are listed in Table 6.3-14. The 
detailed CalEEMod-generated annual summary is in Appendix E. 
Table 6.3-14: Vehicle Traffic Assumptions 
Specifications Assumptions 
Employees 20 
Vehicle trips 4 per shift plus 1 daily misc. trip 
Air district SJVAPCD 
Analysis year 2016 
Land use type General Light Industry 
Annual employee-vehicle traffic emissions, shown in Table 6.3-15, represent a negligible 
increase in emissions and fall well below thresholds established by local, state, and federal 
standards. Therefore, employee vehicle traffic emissions represent a less than significant impact. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-40 
Table 6.3-15: Operational Employee Traffic Emissions Estimates 
Pollutant 
CalEEMod Estimate 
(tons/year) 
Thresholds of Significance 
Reactive organic gases 0.0285 10 tons/year 
Nitrogen oxides 0.1063 10 tons/year 
Respirable particulate 
matter (PM10) 
0.0304 N/A 
See Regulation VIII 
Particulate matter (PM2.5) 0.00914 N/A 
See Regulation VIII 
Carbon monoxide .3236 9 ppm 
6.3.5.5. Cumulative Operational Emissions Impact 
Table 6.3-16 details the total emissions from stationary and mobile sources associated with the 
proposed Endicott project including boiler, fugitive methanol, and vehicle traffic emissions. All 
levels fall below thresholds outlined by the SJVAPCD GAMAQI as well as state and federal 
regulations and, therefore, the overall operational emissions of the proposed Endicott project 
represent a less than significant impact. 
Table 6.3-16: Total Operational Emissions 
Pollutant 
CalEEMod Estimate 
(tons/year) 
Thresholds of Significance 
Reactive organic gases 3.3315 10 tons/year 
Nitrogen oxides 3.6145 10 tons/year 
Respirable particulate 
matter (PM10) 
0.8635 N/A 
See Regulation VIII 
Particulate matter (PM2.5) 0.00914 N/A 
See Regulation VIII 
Carbon monoxide 9.5326 9 ppm 
6.3.5.6. Odor Impacts 
While offensive odors rarely cause any physical harm, they can be very unpleasant, leading to 
considerable distress to the public. Due to the innocuous nature of odor impacts, no requirements 
for their control are included in state or federal air quality regulations; the SJVAPCD has no 
rules or standards related to odor emissions, other than its nuisance rule 35. Any actions related 
to odors are based on citizen complaints to local governments and the SJVAPCD. 
Determinations of significance are based on a review of District complaint records. Significant 
odor problems are defined as: 
¥ More than one confirmed complaint per year averaged over a three year period, or 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-41 
¥ Three unconfirmed complaints per year averaged over a three-year period. 
The most likely source of offensive odors associated with the proposed Endicott project comes 
from a variety of the feedstocks potentially used at the proposed Endicott biofuel production 
facility or stored at Targa. The proposed Endicott facility will have the ability to process a wide 
variety of both edible and inedible lipid feedstocks, most of which are associated with odors that 
are no more offensive than your neighborhood fast-food chain (please refer to the Project 
Description for a more detailed outline of the variety of feedstocks to be employed in the 
Endicott process). However, even the least offensive feedstocks have some potential to produce 
offensive odors should they begin to spoil. 
In order to prevent potential spoilage and, by extension, potential odiferous emissions, all tanks 
will be equipped with nitrogen blanketing systems. The anaerobic environment in a tank purged 
with nitrogen gas inhibits the possibility of decay of organic compounds stored therein. The 
nitrogen blanket serves as a buffer which limits the potential for offensive fugitive emissions. 
Additionally, the proposed facility will operate a thermal oxidizer in compliance with local 
regulations and Best Performance Standards (BPS) as outlined in the districtÕs Climate Change 
Action Plan. All gas/vapor emissions with potential to pose an olfactory impact shall be 
incinerated as stipulated in SJVAPCD Rule 4104. Based on EndicottÕs existing operations and 
lack of odor complaints, combined with design specifications calling for nitrogen blanketing, all 
potential odor impacts have been mitigated to a less than significant impact. 
6.3.5.7. Mitigation Measures 
The following mitigation measures would be implemented to control PM10 emissions: 
AQ-1 Implementation of fugitive dust control measures mandated by SJVACPD Regulation 
VIII. 
AQ-2 Suspend excavation and grading activity when sustained winds exceed 20 miles per 
hour or when gusts exceed 25 miles per hour. 
AQ-3 Install wheel washers for all exiting trucks and equipment leaving the site. 
Although the NOx, CO, and CO2 emissions for the construction period are within the thresholds 
of significance, the following mitigation measures would further reduce emissions: 
AQ-4 Use alternative fuel or catalyst-equipped diesel construction equipment. 
AQ-5 Minimize idling time (e.g., 5-minute maximum) 
AQ-6 Replace fossil-fueled equipment with electrically driven equivalents when possible. 
AQ-7 Limit or curtail construction activity during periods of high ambient pollution. 
All tanks constructed at the proposed Endicott biofuel production facility, as well as Endicott 
Storage tanks at Targa, would have the following design factors incorporated to reduce 
emissions: 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-42 
AQ-8 Primary and Secondary Roof Seals Ð The seals prevent emissions from escaping from 
between the IFR and the tank shell. The primary seal is a metallic band (called a 
shoe) attached to the floating roof. The shoe slides in contact with the tank shell as 
the level of product in the tank rises and falls. The secondary seal is mounted above 
the primary seal. Secondary seals further reduce vapor losses from the gaps between 
the metallic shoe and tank shell. 
AQ-9 Drain Dry Design Ð A drain-dry tank can be completely drained of product using the 
standard pumping systems such that when changing between different product types 
the tank does not need to be cleaned as often. 
AQ-10 Drain Dry Vapor Recovery Unit Ð Vapors associated with the drain-dry operations 
would be extracted and condensed through a PURGIT air pollution condensers 
control system. 
AQ-11 Nitrogen Blanketing Ð Blanketing tank contents with nitrogen gas eliminates 
degradation of organic materials stored therein and acts as a buffer between tank 
contents and potential emissions. 
To address the potential impact that might be caused by certain odiferous feedstocks, the 
proposed Endicott biofuel production facility and storage tanks at Targa will implement the 
following mitigation measures: 
AQ-12 Vapor/Gas emissions from the processing of animal derived feedstocks will be 
controlled using a combination of tank & vessel transfer balancing lines, active 
carbon filtration, nitrogen blanketing and incinerated in a thermal oxidizer. 
AQ-13 All applicable production and storage tanks will be blanketed with nitrogen gas to 
prevent decomposition of stored materials. 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-43 
6.3.6. Air Quality Initial Study Responses 
Table 6.3-17: Air Quality Initial Study Responses 
WOULD THE PROPOSED 
PROJECT: 
Potentially 
Significant 
Impact 
Less-thansignificant 
Impact with 
Mitigation 
Incorporated 
Less-thansignificant 
Impact 
No 
Impact 
AIR QUALITY: Where available, the significance criteria established by the applicable air quality management or 
air pollution control district may be relied upon to make the following determinations. Would the project: 
a) Conflict with or obstruct implementation of 
the applicable air quality plan? 
. . . . 
b) Violate any air quality standard or 
contribute substantially to an existing or 
projected air quality violation? 
. 
. . . 
c) Result in a cumulatively considerable net 
increase of any criteria pollutant for which 
the project region is non-attainment under 
an applicable federal or state ambient air 
quality standard (including releasing 
emissions which exceed quantitative 
thresholds for ozone precursors)? 
. 
. . . 
d) Expose sensitive receptors to substantial 
pollutant concentrations? 
. 
. . . 
e) Create objectionable odors affecting a 
substantial number of people? 
. . . . 
6.3.7. Responses to Initial Study Questions 
6.3.7.1. Air Quality Plan: Less than Significant Impact 
The SJVAPCD has adopted and periodically revises an Attainment Plan that addresses PM10, 
ozone and ozone precursors, (NOx and ROGs). Along with the Attainment Plan, the City of 
Stockton has outlined measures in their 2035 General Plan and EIR to reduce criteria pollutants. 
The Port also calls for measures to reduce criteria pollutants with the Port of Stockton 
Development Plan and EIR. The combined effect of the above plans ensures that when 
incorporated into subsequent projects, they will avoid or reduce impacts and result in reasonable 
further progress toward attainment with air quality standards over time. The SJVAPCD has air 
quality plans set in place to reduce emissions and meet and maintain attainment status of the 
NAAQS and CAAQS. 
Plans are in place for those pollutants for which the district is in nonattainment of federal 
standards (ozone, PM2.5, PM10) or for which they recently achieved attainment status (CO). The 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-44 
SJVAPCD has particulate matter plans available on their website. Compliance with the 
SJVAPCD plans and regulations will ensure that the proposed Endicott project will not conflict 
with or obstruct implementation of the air quality improvement plans. 
The proposed Endicott project would have no impact to the SJVAPCDÕs Air Quality Plan 
because it would not create or cause adverse impacts or alter the current ambient air quality 
status. The proposed Endicott project would adhere to the Air Quality Plan by providing relevant 
and economically feasible mitigation measures as conditional requirements. Monitoring would 
be conducted as prescribed by permit conditions to ensure compliance. 
6.3.7.2. Air Quality Violation: Less than Significant with Mitigation Incorporated 
Air quality violations could occur due to construction or operational emissions. During 
construction, the emissions for ozone precursors NOx and ROG are below the yearly threshold 
and, therefore, pose no significant impact. PM10 would have no impact due to the proposed 
Endicott project conformity with SJVAPCD Regulation VIII for PM10 violations. 
Operations at the proposed Endicott project would have NOx, ROG, CO, and PM10 emissions 
associated with the ISBL production line, production tank emissions, and employee vehicle 
traffic emissions. Emissions would not exceed the SJVAPCD threshold of significance. 
The emissions of ozone precursors NOx and ROG are estimated to be on a level below the 
thresholds of significance set by the SJVAPCD. Ozone violations are typically the result of a 
peak period in emissions of NOx and ROG. For example, many ozone violations occur in the 
afternoon of sunny days following morning Òrush hourÓ traffic which emits large amounts of 
NOx. Because the proposed Endicott project would operate 24 hours a day and 7 days a week, its 
emissions would be incrementally distributed. Because the emissions would be evenly 
distributed over the course of a day (without a peak period), the emissions at any given time are 
limited, and therefore, within prescribed regulations. 
Emissions associated with construction equipment may cause a temporary excedence of certain 
thresholds, in particular, PM. Required mitigation measures, however, would be implemented as 
needed, reducing emissions to less than significant levels. Therefore, air quality violations are 
less than significant with mitigation. 
6.3.7.3. Cumulative Air Quality Impacts: Less than Significant with Mitigation 
Incorporated 
The SJVAPCD GAMAQI addresses cumulative air quality impacts for ozone, PM10, CO, and 
HAPs. Cumulative air quality impacts occur when two or more related individual impacts 
compound to create a net significant impact. For ozone precursors NOx and ROG, the GAMAQI 
recommends cumulative impacts are based on thresholds of significance. 
For PM10, the GAMAQI recommends lead agencies examine PM10 exposure to sensitive 
receptors during earth-disrupting activities by the proposed Endicott project and any other 
projects that may occur in the surrounding area at the same time. Since all projects within the 

6.3 Air Quality 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-45 
SJVAPCD must comply with Regulation VIII for PM10 control and sensitive receptors are not in 
close proximity to the lease area or in the path of prevailing winds, this is considered a less-thansignificant 
impact with mitigation. 
6.3.7.4. Sensitive Receptors: Less than Significant 
The SJVAPCD GAMAQI, Section 3, defines a sensitive receptor as a location where there is a 
reasonable expectation of continuous human exposure to pollutants. Sensitive receptors are 
usually evaluated for more acute, localized pollutants (PM10, SO2, hydrogen sulfide) rather than 
regional pollutants such as ozone precursors (NOx and ROG). 
The closest sensitive receptors to the proposed project site are: 
¥ City Gardens Mobile Home Park is located on the north side of the port waterway in the 
Louis Park neighborhood; and 
¥ George Washington Elementary School is 1.3 miles east of the lease area in Boggs Tract. 
The only significant stationary-source emission from the proposed Endicott project which poses 
a potential risk to sensitive receptors is Methanol from the ISBL production line and production 
tanks. However, computer modeling has determined that concentrations of this chemical at the 
site of identified sensitive receptors falls far below established thresholds. Also, the favorable 
winds at the proposed lease area are from the north so it is unlikely that fugitive emissions would 
ever reach the sensitive receptors located north and east of the proposed lease area. 
Carbon monoxide is the main pollutant of concern for mobile sources in the area. The traffic 
study indicates the proposed Endicott project would not reduce the Level of Service of any 
intersection within the region and, thus, no CO hotspots were identified. As no CO hotspots and 
methanol emissions are projected to disperse to acceptable levels as observed from within 
sensitive receptor areas, the impact on such areas from the proposed Endicott project will be less 
than significant. 
6.3.7.5. Objectionable Odors: Less than Significant Impact with Mitigation 
Incorporated 
Emissions and odors from the proposed Endicott project would be controlled with the BACT 
outlined in the mitigation measures. Odors from the diesel engines operating on the OGVs and 
trucks would be negligible due to their distances from sensitive receptors, spatial and temporal 
distribution due to constant movement, and idling restrictions enforced by the mitigation 
measures and the SJVAPCD. As such the impact of the proposed Endicott project would less 
than significant with mitigation incorporated. 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-47 
migratory birds . . . or any part, nest, or egg of any such bird.Ó (16 USC 703). As authorized by 
the MBTA, the USFWS issues permits to qualified applicants for the following types of 
activities: falconry, raptor propagation, scientific collecting, special purposes (rehabilitation, 
education, migratory game bird propagation, and salvage), take of depredating birds, taxidermy, 
and waterfowl sale and disposal. 
The list of migratory birds includes nearly all bird species native to the United States. The 
MBTA Reform Act of 2004 further defined species protected under the Act and excluded all 
non-native species. The statute was extended in 1974 to include parts of birds, as well as eggs 
and nests. Thus, it is illegal under the MBTA to directly kill, or destroy a nest of, nearly any bird 
species, not just endangered species. Activities that result in removal or destruction of an active 
nest (a nest with eggs or young being attended by one or more adults) would violate the MBTA. 
State Regulations 
California Environmental Quality Act 
Section 15064.7 of the CEQA Guidelines encourages local agencies to develop and publish the 
thresholds that the agency uses in determining the significance of environmental effects caused 
by projects under its review. However, agencies may also rely upon the guidance provided by the 
expanded Initial Study checklist contained in Appendix G of the CEQA Guidelines. Appendix G 
provides examples of impacts that would normally be considered significant. 
An evaluation of whether or not an impact on biological resources would be substantial must 
consider both the resource itself and how that resource fits into the regional or local context. 
Substantial impacts would be those that would diminish, or result in the loss of, an important 
biological resource, or those that would obviously conflict with local, state, or federal resource 
conservation plans, goals, or regulations. Impacts are sometimes locally important but not 
significant under CEQA such a case occurs when impacts result in an adverse alteration of 
existing conditions, but do not substantially diminish, or result in the permanent loss of, an 
important resource on a population-wide or region-wide basis. 
California Endangered Species Act 
The State of California enacted the California Endangered Species Act (CESA) in 1984. CESA 
directs agencies to consult with the California Department of Fish and Wildlife (CDFW) on 
projects or actions that could affect listed species, directs the CDFW to determine whether 
jeopardy would occur, and allows the CDFW to identify Òreasonable and prudent alternativesÓ to 
the project consistent with conserving the species. CESA generally parallels the main provisions 
of FESA, but unlike its federal counterpart, CESA applies the ÒtakeÓ prohibitions to species 
proposed for listing (called candidates by the State). ÒTakeÓ is defined in Section 86 of the 
California Fish and Game (CFG) Code as to Òhunt, pursue, catch, capture, or kill, or attempt to 
hunt, pursue, catch, capture, or kill.Ó Section 2080 of the CFG Code prohibits the taking, 
possession, purchase, sale, and import or export of endangered, threatened, or candidate species, 
unless otherwise authorized by permit or in the regulations. CESA allows the CDFW to 
authorize exceptions to the stateÕs prohibition against take of a listed species (except for 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-48 
designated fully protected species) if the take of a listed species is incidental to carrying out an 
otherwise lawful project that has been approved under CEQA (CFG Code ¤ 2081). 
Fully Protected Species 
The State of California first began to designate species as fully protected prior to the creation of 
CESA and FESA. Lists of fully protected species were initially developed to provide protection 
to those species that were rare or faced possible extinction, and included fish, amphibians and 
reptiles, birds, and mammals. Most fully protected species have since been listed as threatened or 
endangered under CESA and/or FESA. The regulations that implement the Fully Protected 
Species Statute (CFG Code Section 4700) provide that fully protected species may not be taken 
or possessed at any time. Senate Bill 618, amended in 2011, allows CDFW to issue permits 
authorizing the incidental take of fully protected species under CESA, as long as any take 
authorization is issued in conjunction with the approval of a Natural Community Conservation 
Plan that covers the fully protected species. 
California Species of Concern 
In addition to formal listing under FESA and CESA, some species receive additional 
consideration by the CDFW and lead agencies during the CEQA process. Species that may be 
considered for review are included on a list of species of special concern, developed by the 
CDFW. The list tracks species in California whose numbers, reproductive success, or habitat 
may be in decline. 
California Fish and Game Code 
Section 3503.5 of the CFG Code states that it is Òunlawful to take, possess, or destroy any birds 
in the order Falconiformes or Strigiformes (birds of prey) or to take, possess, or destroy the nest 
or eggs of any such bird except as otherwise provided by this code or any regulation adopted 
pursuant theretoÓ. Disturbance activities that result in abandonment of an active bird-of-prey nest 
in areas adjacent to the disturbance may also be considered a violation of the CFG Code. 
California Native Plant Protection Act and California Native Plant Society 
The California Native Plant Protection Act of 1977 (CFG Code Sections 1900-1913) affords the 
California Fish and Game Commission the authority to designate native plants as endangered or 
rare and protects such endangered or rare plants from take. In addition, plants that are not Statelisted, 
but meet the standards for listing are also protected under CEQA (CEQA Guidelines, 
Section 15380). The California Native Plant Society (CNPS) maintains a list of plant species 
native to California that have low population numbers, limited distribution, or are otherwise 
threatened with extinction. Potential impacts to populations of CNPS-listed plants receive 
consideration under CEQA review. The definitions for each of the CNPS listings are below: 
Plant Ranks 
List 1A: Plants presumed extinct in California 
List 1B: Plants rare, threatened, or endangered in California and elsewhere 
List 2A: Plants presumed extinct in California, but more numerous elsewhere 
List 2B: Plants rare, threatened, or endangered in California, but more numerous elsewhere 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-49 
List 3: Plants about which we need more information Ñ A review list 
Threat Ranks 
0.1: Plants are seriously endangered in California 
0.2: Plants are fairly endangered in California 
0.3: Plants are not very endangered in California 
California Lake and Streambed Alteration Agreement 
Sections 1600 through 1616 of the CFG Code require that a Lake and Streambed Alteration 
Program Notification Package be submitted to the CDFW for Òany activity that may substantially 
divert or obstruct the natural flow or substantially change the bed, channel, or bank of any river, 
stream, or lake.Ó The CDFW reviews the proposed actions and, if necessary, submits to the 
applicant a proposal for measures to protect affected fish and wildlife resources. The final 
proposal on which the CDFW and the applicant agree is the Lake and Streambed Alteration 
Agreement. Often, projects that require a Lake and Streambed Alteration Agreement also require 
a permit from the Corps under Section 404 of the CWA. In these instances, the conditions of the 
Section 404 permit and the Lake and Streambed Alteration Agreement may overlap. 
Local Regulations 
City of Stockton Heritage Tree Ordinance 
The City regulates the removal of heritage trees on private and public property (Stockton 
Municipal Code Chapter 16.130). A heritage tree is defined as all valley oaks (Quercus lobata), 
coast live oaks (Quercus agrifolia), and interior live oaks (Quercus wislizenii) with a trunk 
diameter of 16 inches or greater (measured 24 inches above grade). For multiple-trunk trees of 
the species listed above, the combined total diameter of all trunks 6 inches or greater shall be 
used to determine if they meet the 16-inch threshold. 
San Joaquin County Multi-species Habitat Conservation Plan 
The City of Stockton participates in the San Joaquin County Multi-species Habitat Conservation 
Plan (SJMSCP), which provides a way to balance the conservation of open-space areas with the 
need for development within the County. The SJMSCP covers impacts to biological resources 
pursuant to CEQA, CESA, and FESA, and is approved and authorized by the CDFW and 
USFWS. Participation in the SJMSCP streamlines the permitting and mitigation process in the 
event biological resources would be impacted. Due to its location within the City, the proposed 
Endicott project is located within the Òno pay zoneÓ according to the SJMSCP habitat maps. This 
means there is no fee for project proponents in this area to participate in the program. 
6.4.1.2. Required Permits and Approvals 
No biological resource permits are required for the proposed Endicott project. 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-50 
6.4.2. Methodology 
6.4.2.1. Literature Review 
Prior to performing the biological field survey, documentation relevant to the proposed project 
area, pipeline route and surrounding area was reviewed and a special-status species list was 
prepared for the project. The special-status species list includes species identified from record 
searches for the U.S. Geological Survey 7.5-minute Stockton West, Stockton East, Manteca, 
Lathrop, Union Island, Holt, Terminous, Lodi South, and Waterloo topographic quadrangles. 
Special-status species include all federally and State-listed endangered and threatened species, 
candidates for listing, species proposed for listing, fully protected species, State species of 
concern, species protected under other regulations (e.g., MBTA), species listed as rare or 
endangered by the CNPS, and species that receive special consideration during environmental 
review under CEQA. 
Sources of information that were used to compile the species list included the USFWS and 
NMFS endangered species lists, the CDFW California Natural Diversity Data Base (CNDDB), 
and the CNPS species lists (online version) for the quadrangles listed above. (See Figure 6.4-1 
California Natural Diversity Data Map) 
6.4.2.2. Field Survey 
TRC biologist, Michael Farmer, conducted a field survey of the project area and pipeline route 
on July 24, 2013. The project locations were systematically surveyed on foot to identify all 
sensitive habitats and determine the potential for the project locations to support each specialstatus 
species identified from the record searches. Each speciesÕ potential for occurrence was 
based on the presence or absence of general habitat requirements (nesting or foraging habitat, 
specific soil type, permanent water source, etc.). During the field survey, all biological 
communities were characterized and the observed plant and wildlife species were recorded. 
6.4.3. Environmental Setting 
The approximately 4.91+/- acre proposed lease area is comprised of mostly barren ground with 
interspersed patches of vegetation. Russian thistle (Salsola tragus) was the dominant plant 
species within the proposed project area during the field survey. Other identified species include 
milk thistle (Silybum marianum), cudweed (Gnaphalium sp.), Bermuda grass (Cynodon 
dactylon), gumweed (Grindelia sp.), and Jimson weed (Datura stramonium). All of these 
species are common ruderal (weedy) species typically found growing in disturbed places. Some 
of the vegetation was dead or stressed with twisted and curled leaves and stems, indicating that 
herbicides may be used for vegetation management purposes. The interior of the lease area lacks 
trees and shrubs; however, a mature ash tree (Fraxinus sp.) and a small cluster of unhealthy 
mature cottonwoods (Populus fremontii) occur along the western parcel boundary and in the 
northwest corner of the lease area, respectively. 
Tire tracks are prevalent in the southern and western portions of the lease and two stockpiles of 
dirt, gravel, asphalt and other debris occur in the northwest portion of the lease area. A dump 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-51 
truck was observed by TRC staff dumping dirt on the stockpile during a July 2013 lease area 
inspection. 
Wildlife activity was very limited during the field survey, most likely because of the disturbed 
nature of the lease area and surrounding port parcels and lack of habitat diversity. Wildlife 
species observed on and adjacent to the site include western fence lizard (Sceloporus 
occidentalis), cliff swallow (Petrochelidon pyrrhonota), western scrub jay (Aphelocoma 
californica), NuttallÕs woodpecker (Picoides nuttallii), and SwainsonÕs hawk (Buteo swainsoni). 
Additionally, multiple burrows were observed throughout the lease area and appear consistent 
with ground squirrel (Spermophilus beecheyi) burrows and other small rodents such as California 
vole (Microtus californicus), although no squirrels or voles were seen. 
6.4.3.1. Special-status Species 
As discussed above, the special-status plant and wildlife species analyzed for the proposed 
Endicott project were identified through the review of existing documentation relevant to the 
lease area and surrounding area. Table 6.4-1: Special-status Species Potentially Occurring on the 
Proposed Lease Area lists the regulatory status, habitat requirements, and potential for 
occurrence on the site for each species considered in the assessment. Figure 6.4-1: California 
Natural Diversity Data Base Map depicts the locations of special-status species recorded in the 
CNDDB within 5 miles of the proposed project area. The USFWS list for the Stockton West 
quadrangle, in which the project area occurs, contains the same species listed on the lists 
generated for the surrounding eight quadrangles. Therefore, only the list for the Stockton West 
quadrangle is included. 
6.4.3.2. Special-status Plants 
Due to presumed vegetation management practices and/or the lack of suitable habitats on the 
assessed land, none of the special-status plant species known to occur in the vicinity of the 
proposed project have the potential to occur. For these reasons, the proposed Endicott project 
would have no impact on special-status plant species. 
6.4.3.3. Special-status Wildlife 
Based on the review of literature relevant to the project and surrounding areas along with the 
field survey, several special-status wildlife species have the potential to occur. However, due to 
the disturbed nature of the project areas and the lack of habitat diversity, special-status species 
with the potential to occur on the lease area are limited to avian species. 
Northern Harrier 
The northern harrier is a slim, long-winged, long-tailed, raptor of open country. It can be found 
in annual grasslands in the Central Valley up to the lodgepole pine belt and alpine meadow 
habitats. Northern harriers are seldom found in wooded areas. This hawk nests on the ground in 
shrubby vegetation, usually at the edge of a marsh. Most of the nests are found in emergent 
wetlands or along rivers or lakes, but it may also nest in grasslands, grain fields, or on sage brush 
flats that are several miles from water. Harriers usually perch on the ground, but will use fence 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-52 
posts or other low perches and occasionally trees (Johnsgard, 1990). Northern harriers feed 
mainly on voles and other small mammals, birds, frogs, small reptiles, some crustaceans, and 
insects. Although no northern harriers were observed during the field survey, the locations 
reviewed provide marginal foraging and nesting habitat. 

6.4 Biological Resources 
6-54 
Table 6.4-1: Special-status Species Potentially Occurring on the Proposed Lease Area 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
Plants 
Alkali milk-vetch 
(Astragalus tenervar. tener) 
1B.2 Playas, valley and foothill grasslands, vernal pools; 
typically in alkaline soils; blooms March through 
June. 
None; disturbed nature of the site 
and lack of suitable habitat 
preclude the occurrence of this 
species on the project locations. 
Big tarplant 
(Blepharizonia plumosa) 
1B.1 Valley and foothill grassland; blooms July through 
October. 
None; disturbed nature of the site 
and lack of suitable habitat 
preclude the occurrence of this 
species on the project locations. 
Bristly sedge 
(Carex comosa) 
2B.1 Freshwater marshes and swamps, and valley and 
foothill grasslands; blooms May through 
September. 
None; disturbed nature of the site 
and lack of suitable habitat 
preclude the occurrence of this 
species on the project locations. 
Delta button-celery 
(Eryngium racemosum) 
SE, 1B.1 Vernally wet clay depressions within riparian 
scrub; blooms June through October. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Delta mudwort 
(Limosella subulata) 
2B.1 Freshwater marshes and swamps; blooms May 
through August. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Delta tule pea 
(Lathyrus jepsonii var. 
jepsonii) 
1B.2 Freshwater marshes and swamps; blooms May 
through July. 
None; there is no suitable habitat 
for this species on the project 
locations. 

6.4 Biological Resources 
6-55 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
Heartscale 
(Atriplex cordulata) 
1B.2 Chenopod scrub, meadows and seeps, 
saline/alkaline valley and foothill grasslands; 
blooms April through October. 
None; disturbed nature of the site 
and lack of suitable habitat 
preclude the occurrence of this 
species on the project locations. 
MasonÕs lilaeopsis 
(Lilaeopsis masonii) 
SR, 1B.1 Riparian areas, freshwater and brackish marshes 
and swamps; blooms April through November. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Palmate-bracted birdÕsbeak 
(Chloropyron palmatum) 
FE, SE, 1B.1 Chenopod scrub, alkaline valley and foothill 
grasslands; blooms May through October. 
None; disturbed nature of the site 
and lack of suitable habitat 
preclude the occurrence of this 
species on the project locations. 
Recurved larkspur 
(Delphinium recurvatum) 
1B.2 Chenopod scrub, cismontane woodland, valley and 
foothill grasslands; blooms March through June. 
None; disturbed nature of the site 
and lack of suitable habitat 
preclude the occurrence of this 
species on the project locations. 
Round-leaved filaree 
(California macrophylla) 
1B.1 Valley and foothill grasslands, cismontane 
woodlands; blooms March through May 
None; disturbed nature of the site 
and lack of suitable habitat 
preclude the occurrence of this 
species on the project locations. 
SanfordÕs arrowhead 
(Sagittaria sanfordii) 
1B.2 Freshwater marshes and swamps; blooms May 
through October. 
None; there is no suitable habitat 
for this species on the project 
locations. 
San Joaquin spearscale 
(Atriplex joaquiniana) 
1B.2 Chenopod scrub, playas, meadows and seeps, 
alkaline valley and foothill grasslands; blooms 
April through October. 
None; disturbed nature of the site 
and lack of suitable habitat 
preclude the occurrence of this 
species on the project locations. 

6.4 Biological Resources 
6-56 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
Slough thistle 
(Cirsium crassicaule) 
1B.1 Chenopod and riparian scrubs, and marshes and 
swamps; blooms May through August. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Suisun Marsh aster 
(Symphyotrichum lentum) 
1B.2 Freshwater marshes and swamps; blooms May 
through November. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Watershield 
(Brasenia schreberi) 
2B.3 Freshwater marshes and swamps; blooms June 
through September. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Woolly rose-mallow 
(Hibiscus lasiocarpos var. 
occidentalis) 
1B.2 Freshwater marshes and swamps; blooms June 
through September. 
None; there is no suitable habitat 
for this species on the project 
locations. 
WrightÕs trichocoronis 
(Trichocoronis wrightii 
var. wrightii) 
2B.1 Riparian forests, vernal pools, meadows and seeps, 
and marshes and swamps; blooms Mayt through 
September. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Invertebrates 
Valley elderberry longhorn 
beetle 
(Desmocerus californicus 
dimorphus) 
FT Blue elderberry shrubs. None; there are no elderberry 
shrubs on the project locations. 
Vernal pool fairy shrimp 
(Branchinecta lynchi) 
FT Vernal pools, seasonal wetlands, and other 
seasonal freshwater habitats. 
None; there is no suitable habitat 
for this species on the project 
locations. 

6.4 Biological Resources 
6-57 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
Vernal pool tadpole shrimp 
(Lepidurus packardi) 
FE Vernal pools, seasonal wetlands, and other 
seasonal freshwater habitats. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Fish 
Central Valley spring-run 
Chinook salmon 
(Oncorhynchus 
tshawytscha) 
FT, ST Sacramento and San Joaquin rivers and their 
tributaries. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Central Valley steelhead 
(Oncorhynchus mykiss) 
FT, CH Sacramento and San Joaquin rivers and their 
tributaries. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Delta smelt 
(Hypomesus 
transpacificus) 
FT, SE, CH Sacramento and San Joaquin rivers and their 
tributaries, but species is usually concentrated in 
Delta and Suisun Bay areas. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Green sturgeon 
(Acipenser medirostris) 
FT Sacramento and Feather rivers and their tributaries. None; there is no suitable habitat 
for this species on the project 
locations. 
Sacramento River winterrun 
Chinook salmon 
(Oncorhynchus 
tshawytscha) 
FE, SE Sacramento River and its tributaries. None; there is no suitable habitat 
for this species on the project 
locations. 

6.4 Biological Resources 
6-58 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
Amphibians/Reptiles 
California horned lizard 
(Phrynosoma coronatum 
frontale) 
CSC Inhabits open oak and coniferous woodlands, 
grasslands, and riparian areas. Species generally 
prefers sandy-soil types and often observed in 
rocky areas or on outcroppings. 
None; there is no suitable habitat 
for this species on the project 
locations. 
California red-legged frog 
(Rana aurora draytonii) 
FT, CSC Inhabits lowlands and foothills in or near 
permanent deep water with dense growth of 
emergent and woody riparian vegetation, bordering 
permanent and semi-permanent ponds, ponded 
streams, marshes, and springs. Upland habitat 
surrounding breeding areas is important for shelter 
during dispersal and estivation. Species is believed 
to have been extirpated from Central Valley floor. 
None; there is no suitable habitat 
for this species on the project 
locations. 
California tiger salamander 
(Ambystoma californiense) 
FT, ST Ponded water required for breeding. Adults spend 
summer in small-mammal burrows. Species range 
extends from the Central Valley and Sierra Nevada 
foothills from Yolo to Colusa counties south to 
Tulare County and in coastal valley and foothills 
from Sonoma to Santa Barbara counties, typically 
below 1,500 feet elevation. 
None; there is no suitable habitat 
for this species on the project 
locations. 

6.4 Biological Resources 
6-59 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
Giant garter snake 
(Thamnophis gigas) 
FT, ST Prefers freshwater marsh and low-gradient stream 
habitats, including extensive rice fields in the 
Central Valley, with sufficient prey base of frogs, 
tadpoles, and small fish. Has adapted to drainage 
canals and irrigation ditches surrounding 
farmlands. Habitat requirements consist of 1) 
adequate water during the snakeÕs active season 
(early spring through mid-fall) to provide food and 
cover; 2) emergent, herbaceous wetland vegetation 
such as cattails and bulrushes for escape cover and 
foraging habitat during the active season; 3) grassy 
banks and openings in waterside vegetation for 
basking; and 4) higher elevation uplands for cover 
and refuge from flood waters during the snakeÕs 
dormant season in the winter. Giant garter snakes 
are typically absent from wetlands with sand, 
gravel, or rock substrates. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Western pond turtle 
(Emys marmorata) 
CSC Found throughout the State inhabiting agricultural 
ponds, permanent pools along intermittent 
drainages, irrigation canals, low-gradient rivers 
and streams with emergent vegetation and suitable 
basking sites; and their associated upland habitats. 
None; there is no suitable habitat 
for this species on the project 
locations. 

6.4 Biological Resources 
6-60 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
Western spadefoot toad 
(Spea hammondii) 
CSC Inhabits lowlands in open areas with sandy or 
gravelly soils in a variety of habitats, including 
mixed woodlands, grasslands, chaparral, sandy 
washes, river floodplains, alluvial fans, playas, 
alkali flats, foothills, and mountains. Breeds from 
January through May in temporary pools and quiet 
streams. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Birds 
Bank swallow 
(Riparia riparia) 
ST Breeding ranges are restricted to the Sacramento 
Valley (Sacramento and Feather rivers), 
northeastern California, and small areas of the 
central and north coast. Inhabits riparian lowlands 
and nests in colonies. Requires vertical cliffs or 
soft banks with fine-textured soils near streams, 
rivers, lakes, and ocean for nesting. Suitable 
nesting habitat declining from flood-control 
measures (river channelization and artificial bank 
stabilization). Winters in South America. 
None; there is no suitable habitat 
for this species on the project 
locations. 
Greater sandhill crane 
(Grus canadensis tabida) 
ST Nests in wet meadows interspersed with emergent 
marsh habitat in northeastern California. Winters 
in agricultural croplands, marshlands, and irrigated 
pastures. 
None, there is no suitable habitat 
for this species on the project 
locations. 
Northern harrier 
(Circus cyaneus) 
CSC Forages for small birds and mammals over 
meadows, farmlands, grasslands, and rangelands. 
Perches on ground or low fence posts; usually seen 
flying low over ground when foraging. Nests on 
the ground in fields or along the edges of marshes. 
Low; marginal foraging and 
marginal nesting habitat exist on 
the project locations. 

6.4 Biological Resources 
6-61 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
SwainsonÕs hawk 
(Buteo swainsoni) 
ST Nests in isolated trees or riparian woodlands 
adjacent to suitable foraging habitat such as 
agricultural fields and grasslands. 
Low; marginal nesting habitat on 
the project locations, but higherquality 
nest trees occur adjacent 
to the project locations. The 
project locations provide marginal 
foraging habitat and one 
SwainsonÕs hawk was observed 
soaring adjacent to the project 
locations during the field survey. 
Tricolored blackbird 
(Agelaius tricolor) 
CSC Colonial species in the Central Valley and vicinity. 
Nests primarily in dense blackberry thickets, 
cattails, and tules. 
None, there is no suitable habitat 
for this species on the project 
locations. 
Western burrowing owl 
(Athene cunicularia 
hypugaea) 
CSC Nests in subterranean burrows often created by 
ground squirrels within open, dry grasslands; 
deserts; and scrublands characterized by lowgrowing 
vegetation. 
Low; marginal nesting and 
foraging habitat occur on the 
project locations. There was no 
evidence of the species observed 
during the field survey. 
White-tailed kite 
(Elanus leucurus) 
CFP Found in open grasslands, savanna, open 
woodlands, marshes, desert grassland, partially 
cleared lands, and cultivated fields with scattered 
trees for nesting and perching. Nests in large 
shrubs or trees often in riparian corridors where it 
competes with other raptors for suitable nest sites. 
Low; marginal nesting habitat on 
the project locations, but higherquality 
nest trees occur adjacent 
to the project locations. The 
project locations provide marginal 
foraging habitat. 

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6-62 
Species 
Regulatory 
Status1 
Habitat Requirements Potential for Occurrence 
Mammals 
Riparian brush rabbit 
(Sylvilagus bachmani 
riparius) 
FE, SE Riparian habitats along the San Joaquin River. None, there is no suitable habitat 
for this species on the project 
locations. 
San Joaquin kit fox 
(Vulpes macrotis mutica) 
FE, ST Open, dry grassland, shrub, and open forest 
habitats in the San Joaquin Valley and surrounding 
foothills. 
None, there is no suitable habitat 
for this species on the project 
locations. 
1Definitions 
Federal California California Native Plant Society 
FE Federally 
endangered 
SE State endangered 1B Rare, threatened, or endangered in California 
and elsewhere 
FT Federally 
threatened 
ST State threatened 2B Plants rare, threatened, or endangered in 
California, but more numerous elsewhere 
CH Critical habitat SR State rare 0.1 Plants are seriously endangered in California 
CSC California species 
of concern 
0.2 Plants are fairly endangered in California 
CFP California fully 
protected 
0.3 Plants are not very endangered in California 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-63 
SwainsonÕs Hawk 
SwainsonÕs hawk is a long-distance migrant with nesting grounds in western North America. The 
SwainsonÕs hawk population that nests in the Central Valley winters primarily in Mexico, while 
the population that nests in the interior portions of North America winters in South America 
(Bradbury et al., in prep.). SwainsonÕs hawks arrive in the Central Valley between March and 
early April to establish breeding territories. Breeding occurs from late March to late August, 
peaking in late May through July (Zeiner et al., 1990). In the Central Valley, SwainsonÕs hawks 
nest in isolated trees, small groves, or large woodlands next to open grasslands or agricultural 
fields. This species typically nests near riparian areas; however, it has been known to nest in 
urban areas as well. Nest locations are usually in proximity to suitable foraging habitats, which 
include fallow fields, annual grasslands, irrigated pastures, alfalfa and other hay crops, and lowgrowing 
row crops. SwainsonÕs hawks leave their breeding grounds to return to their wintering 
grounds in late August or early September (Bloom and De Water, 1994). 
While the ash and cottonwood trees within the project area provide marginal nesting habitat, the 
mature black walnut and cottonwood trees located immediately north of the project area along 
the San Joaquin River provide better nesting opportunities for this species. Although the project 
area provides lower-quality foraging habitat compared to the fallow fields, row crops, and annual 
grasslands in the vicinity of the project area, SwainsonÕs hawk could still forage on the property. 
As previously mentioned, one SwainsonÕs hawk was observed soaring near the project area 
during the field survey. 
Western Burrowing Owl 
Western burrowing owl is a small, ground-dwelling owl that occurs in western North America 
from Canada to Mexico, and east to Texas and Louisiana. Although in certain areas of its range 
western burrowing owls are migratory, the owls are predominantly non-migratory in California 
(Zeiner et al., 1990). The breeding season for western burrowing owls occurs from February to 
August, peaking in April and May (Zeiner et al., 1990). Western burrowing owls nest in burrows 
in the ground, often in old ground squirrel burrows. This owl is also known to use artificial 
burrows, including pipes, culverts, and nest boxes. 
The larger burrows observed throughout the lease area are the appropriate size for western 
burrowing owl use; however, no sign of the species was identified on the project locations during 
the field survey. Additionally, the relatively unvegetated portions of the project locations provide 
suitable foraging habitat. 
White-tailed Kite 
The white-tailed kite is a medium-sized raptor that is a yearlong resident in coastal and valley 
lowlands in California. White-tailed kites are monogamous and breed from February to October, 
peaking from May to August (Zeiner et al., 1990).This species nests near the top of dense oak, 
willow, or other large trees. White-tailed kites are typically found foraging in open grasslands, 
farmlands, meadows, and emergent marshes where they prey mostly on small mammals. 
Comparable to the SwainsonÕs hawk analysis, marginal nesting habitat occurs within the project 
area with higher-quality nesting habitat just north of the lease area along the San Joaquin River. 
The project locations provide foraging habitat for white-tailed kite even through better 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-64 
opportunities occur in the fallow fields, row crops, and annual grasslands in the vicinity of the 
lease area. 
Other Bird Species Protected by the MBTA 
In addition to the bird species discussed above, the project locations provides nesting habitat for 
bird species protected solely by the MBTA, such as northern mockingbirds and mourning doves. 
While the project area supports very few trees, should vegetation management practices on the 
project area cease or not be implemented on a routine basis, the extent of nesting habitat would 
increase significantly as the herbaceous plant species become re-established. Although nesting 
habitat provided by vegetation was limited during the inspection, some common birds such as 
killdeer (Charadrius vociferus) are known to nest on the ground. 
Several cliff swallows were observed flying in the vicinity of the project areas and perched under 
the Navy Drive bridge immediately north of the project area. While it was difficult to detect any 
mud nests under the bridge during the survey, there is a high potential for a nesting cliff swallow 
colony to utilize the bridge. 
6.4.3.4. Wetlands and Jurisdictional Waters 
Based on the field survey, there are no wetlands, drainage ditches, or other water features on the 
project areas. There was no evidence of wetland hydrology or hydrophytic vegetation observed. 
6.4.4. Standards of Significance 
Under CEQA, an impact to biological resources is considered significant if the project would: 
. Have a substantial adverse effect, either directly or through habitat modifications, on any 
species identified as a candidate, sensitive, or special-status species in local or regional 
plans, policies, or regulations, or by the CDFW or USFWS; 
. Have a substantial adverse effect on any riparian habitat or other sensitive natural 
community identified in local or regional plans, policies, and regulations, or by the 
CDFW or USFWS; 
. Have a substantial adverse effect on federally protected wetlands as defined by Section 
404 of the CWA (including, but not limited to, marsh, vernal pool, coastal, etc.) through 
direct removal, filling, hydrological interruption, or other means; 
. Interfere substantially with the movement of any native resident or migratory fish or 
wildlife species or with established native resident or migratory wildlife corridors, or 
impede the use of native wildlife nursery sites; 
. Conflict with any local policies or ordinances protecting biological resources such as a 
tree preservation policy or ordinance; and/or 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-65 
. Conflict with the provisions of an adopted habitat conservation plan, natural community 
conservation plan, or other approved local, regional, or State habitat conservation plan. 
In the evaluation process, it is noted that Section 15380 of the CEQA Guidelines defines 
endangered, rare, or threatened species as follows: 
1)ÒEndangeredÓ when its survival and reproduction in the wild are in immediate 
jeopardy from one or more causes, including loss of habitat, over-exploitation, predation, 
competition, disease, or other factors; or 
2)ÒRareÓ (all animals designated as rare by the Fish and Game Commission prior to 
January 1, 1985 were automatically reclassified as threatened by Fish and Game Code 
Sec. 2067) when either: 
(a)Although not presently threatened with extinction, the species is existing in 
such small numbers throughout all or a significant portion of its range that it may 
become endangered if its environment worsens; or 
(b)The species is likely to become endangered within the foreseeable future 
throughout all or a significant portion of its range and may be considered 
ÒthreatenedÓ as that term is used in the Federal Endangered Species Act. 
(c)A species of animal or plant shall be presumed to be endangered, rare, or 
threatened, if it is listed in: 
(1) Sections 670.2 or 670.5, Title 14, California Administrative Code of 
Regulations; or 
(2) Title 50, Code of Federal Regulations Sections 17.11 or 17.2 pursuant 
to the Federal Endangered Species Act as rare, threatened, or 
endangered. 
(d)A species not included in any listing identified in subsection (c) shall 
nevertheless be considered to be rare or endangered if the species can be shown 
to meet the criteria in subsection (b). 
(e)This definition shall not include any species of the Class Insecta, which is a 
pest whose protection under the provisions of CEQA would present an 
overwhelming and overriding task to man as determined by: 
(1) The Director of Food and Agriculture with regard to economic pests; 
or 
(2) The Director of Health Services with regard to health risks. 

6.4 Biological Resources 
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Initial Study 6-66 
6.4.5. Impacts and Mitigation Measures 
Suitable habitat for protected or sensitive species on the project areas is limited to marginal 
nesting and foraging habitat for SwainsonÕs hawk, western burrowing owl, white-tailed kite, and 
other birds protected by the MBTA. Although no bird species were observed actively nesting or 
foraging on the project areas during the field inspection, suitable nesting and foraging habitat 
could potentially be impacted by the implementation of the proposed project. Furthermore, the 
proposed Endicott project would participate in the San Joaquin Council of Governments 
(SJCOG) San Joaquin County Multi-species Habitat Conservation Plan, which would further 
ensure potential impacts would be mitigated to a less-than-significant level concerning specialstatus 
species. The mitigation measure below addresses the conservation guidelines that shall be 
implemented to mitigate for project-related potential impacts. 
BIO-1 Subsequent to contacting the SJCOG, a biologist retained by the SJCOG will perform 
a pre-construction survey of the site prior to any project-related ground disturbance to 
verify vegetation types affected by the project and to determine if any species covered 
by the San Joaquin County Multi-species Habitat Conservation Plan occur on the site. 
The results of the pre-construction survey will determine which Incidental Take 
Minimization Measures (if any) will be required for project approval. Incidental Take 
Minimization Measures have been established for each species covered by the Plan to 
ensure that all impacts to covered species are minimized and mitigated appropriately 
under FESA, CESA, and CEQA. 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-67 
6.4.6. Biological Resources Initial Study Responses 
Table 6.4-2: Biological Resources Initial Study Responses 
WOULD THE PROJECT: 
Potentially 
Significant 
Impact 
Less Than 
Significant 
Impact with 
Mitigation 
Incorporated 
Less Than 
Significant 
Impact 
No 
Impact 
a) Have a substantial adverse effect, 
either directly or through habitat 
modifications, on any species identified 
as a candidate, sensitive, or specialstatus 
species in local or regional 
plans, policies, or regulations, or by the 
California Department of Fish and 
Game or U.S. Fish and Wildlife 
Service? 
. . . . 
b) Have a substantial adverse effect on 
any riparian habitat or other sensitive 
natural community identified in local or 
regional plans, policies, regulations, or 
by the California Department of Fish 
and Game or U.S. Fish and Wildlife 
Service? 
. . . . 
c) Have a substantial adverse effect on 
federally protected wetlands as defined 
by Section 404 of the Clean Water Act 
(including, but not limited to, marsh, 
vernal pool, coastal, etc.) through 
direct removal, filling, hydrological 
interruption, or other means? 
. . . . 
d) Interfere substantially with the 
movement of any native resident or 
migratory fish or wildlife species or with 
established native resident or migratory 
wildlife corridors, or impede the use of 
native wildlife nursery sites? 
. . . . 
e) Conflict with any local policies or 
ordinances protecting biological 
resources, such as a tree preservation 
policy or ordinance? 
. . . . 
f) Conflict with the provisions of an 
adopted Habitat Conservation Plan, 
Natural Community Conservation Plan, 
or other approved local, regional, or 
state habitat conservation plan? 
. . . . 

6.4 Biological Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-68 
6.4.7. Responses to Initial Study Questions 
Species Impacts: Less than Significant with Mitigation Incorporated 
The development of the proposed Endicott project area would permanently remove marginal 
nesting and foraging habitat for SwainsonÕs hawk, western burrowing owl, white-tailed kite, and 
other birds protected by the MBTA. The projectÕs participation in the San Joaquin County Multispecies 
Habitat Conservation Plan would reduce potential impacts to sensitive birds to a lessthan-
significant level. 
Riparian and Other Sensitive Habitats: No Impact 
There are no riparian habitats or sensitive natural communities within the proposed project area. 
The proposed project area is highly disturbed and composed of barren land and scattered ruderal 
vegetation. The proposed Endicott project would have no impact on riparian and other sensitive 
habitats. 
Federally Protected Wetlands: No Impact 
There are no wetland features on the project areas. Therefore, the proposed Endicott project 
would have no impact on federally protected wetlands. 
Interfere with Movement of Native Wildlife: No Impact 
Although the lease area is along the Pacific Flyway, an established air route of waterfowl and 
other birds migrating between wintering grounds in Central and South America and nesting 
grounds in Pacific Coast states and provinces of North America, the small size of the lease area 
and lack of aquatic features and higher-quality vegetation communities preclude migratory bird 
species from using the lease area as a stopover during their migration. The lack of aquatic 
features would also eliminate potential project-related impacts to resident and migratory fish. 
Although the project areas are immediately adjacent to the San Joaquin River corridor, they are 
surrounded on all other sides by industrial land uses and do not link the river corridor to other 
natural habitats. Therefore, the proposed project areas do not provide wildlife movement 
corridors and the project will have no impact on the movement of terrestrial or aquatic wildlife. 
Conflict with Local Policies: No Impact 
The Endicott project is covered by the San Joaquin County Multi-species Habitat Conservation 
Plan and is in a Òno pay zone,Ó meaning that no fee payments would be required to compensate 
for loss of biological resources under the Plan. The project would participate in the Plan and 
consult with plan administrators where necessary to comply with all local policies or ordinances 
protecting biological resources. 
Conflict with Conservation Plans: No Impact 
As discussed above, the Endicott project areas are covered by the San Joaquin County Multispecies 
Habitat Conservation Plan. The proposed project would participate in the Plan and would 
not conflict with the Plan or other approved local, regional, or state habitat conservation plans. 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-69 
6.5 Cultural Resources 
Cultural resources are historic and prehistoric archaeological sites, historic buildings and 
structures, and resources of traditional cultural significance to Native Americans and other 
groups. This section reviews the proposed Endicott projectÕs potential impact to cultural 
resources. Figure 6.5-1 depicts the cultural-archaeological area of potential effect. 
6.5.1. Background 
6.5.1.1. Regulatory Context 
Cultural resources in the State of California are recognized as non-renewable resources that 
require management to assure their benefit to presentÑand futureÑCalifornians. Therefore, 
cultural resources management work conducted as part of any proposed undertaking must 
comply with applicable federal, state, and/or local regulations designed to protect the cultural 
heritage within the proposed project area. 
Federal Regulations 
National Historic Preservation Act 
Enacted in 1966, the National Historic Preservation Act (NHPA) has become the foundation and 
framework for historic preservation in the United States. The NHPA authorizes the Secretary of 
the Interior to expand and maintain a National Register of Historic Places, establishes an 
Advisory Council on Historic Preservation as an independent federal entity, requires federal 
agencies to take into account the effects of their undertakings on historic properties, affords the 
Advisory Council on Historic Preservation a reasonable opportunity to comment on any 
undertaking that may affect historic properties listed, or eligible for listing, in the National 
Register of Historic Places, and makes the heads of all federal agencies responsible for the 
preservation of historic properties owned or controlled by their agencies. 
Section 106 of the NHPA governs federal regulations for cultural resources. The goal of the 
Section 106 process is to offer a measure of protection to sites that are determined eligible for 
listing on the National Register of Historic Places. The criteria for determining National Register 
eligibility are found in 36 Code of Federal Regulations (CFR) Part 60. 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-71 
State Regulations 
Discretionary actions undertaken by state or local governments in California, unless otherwise 
exempted, must comply with the CEQA Guidelines, Sections 21083.2 and 15064.5. Enacted in 
1971, CEQA directs lead agencies to first determine whether a cultural resource is a Òhistorically 
significantÓ cultural resource. In the protection and management of the cultural environment, 
CEQA Guidelines provide definitions and standards for cultural resources management. The 
term Òhistorical resourceÓ is defined as follows: 
(1) A resource listed in, or determined to be eligible by the State Historical 
Resources Commission, for listing in the California Register of Historical 
Resources. 
(2) A resource included in a local register of historical resources or identified as 
significant in a historical resource survey shall be presumed to be historically 
or culturally significant. Public agencies must treat any such resource as 
significant unless the preponderance of evidence demonstrates that it is not 
historically or culturally significant. 
(3) Any object, building, structure, site area, record, or manuscript, which a lead 
agency determines to be historically significant or significant in the 
architectural, engineering, scientific, economic, agricultural, educational, 
social, political, military, or cultural annals of California may be considered to 
be a historical resource, provided the lead agencyÕs determination is supported 
by substantial evidence in light of the whole record. Generally, a cultural 
resource shall be considered by the lead agency to be Òhistorically significantÓ 
if the resource meets the criteria for listing on the California Register of 
Historical Resources, including the following: 
a. Is associated with events that have made a significant contribution to the 
broad patterns of CaliforniaÕs history and cultural heritage; 
b. Is associated with the lives of persons important in our past; 
c. Embodies the distinctive characteristics of a type, period, region, or 
method of construction, or represents the work of an important creative 
individual, or possesses high artistic values; or 
d. Has yielded, or may be likely to yield, information important in 
prehistory or history. 
The fact that a resource is not listed in, or determined to be eligible for listing in the California 
Register of Historical Resources, or is not included in a local register of historical resources, or 
identified in a historical resources survey, does not preclude a lead agency from determining that 
the resource may be a historical resource [Title 14 CCR Section 15064.5(1) (California, 2011)]. 
As defined in Section 15064.5(1) of the CEQA Guidelines, a Òunique archaeological resourceÓ 
is: 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-72 
An archaeological artifact, object, or site about which it can be clearly 
demonstrated that, without merely adding to the current body of knowledge, there 
is a high probability that it meets any of the following criteria: 
(1) Contains information needed to answer important scientific research 
questions and that there is a demonstrable public interest in that 
information. 
(2) Has a special and particular quality such as being the oldest of its type or 
the best available example of its type. 
(3) Is directly associated with a scientifically recognized important prehistoric 
or historical event or person [Public Resources Code Section 21083.2(g)]. 
A project with an effect that may cause a substantial adverse change in the significance of a 
historical resource or unique archaeological resource is a project that may have a significant 
effect on the environment per the CEQA Guidelines, Section 21083.2. Effects on cultural 
properties that qualify as historical resources or unique archaeological resources can be 
considered adverse if they involve physical demolition, destruction, relocation, or alteration of 
the resource or its immediate surroundings such that the significance of a historical resource 
would be materially impaired. 
The statutes and guidelines cited above specify how cultural resources are to be managed in the 
context of projects subject to CEQA. Archival and field surveys must be conducted and 
identified cultural resources must be inventoried and evaluated in prescribed ways per the CEQA 
Guidelines, Section 21083.2. 
Prehistoric and historical resources deemed Òhistorically significantÓ must be considered in 
project planning and development. As well, any proposed undertaking that may affect 
Òhistorically significantÓ cultural resources must be submitted to the State Historic Preservation 
Officer for review and comment prior to project approval by the responsible agency and prior to 
construction. The CEQA Guidelines detail methods by which significant effects may be 
mitigated and discuss procedures for treatment of human remains discovered in the course of 
project development. 
The California Office of Historic Preservation administers the California Register program, the 
California Register of Historical Landmarks, and California Points of Local Historical Interest 
programs. The State Historic Preservation Officer enforces the designation and protection 
process and is the head of the California Office of Historic Preservation. The California Office of 
Historic Preservation ensures that the state has a qualified historic preservation review 
commission, maintains a system for surveys and inventories, and provides for adequate public 
participation in its activities. The Office of Historic Preservation also administers the Certified 
Local Government program for the State of California. 
Native American Consultation 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-73 
TRC contacted the Native American Heritage Commission (NAHC) regarding the presence of 
burials and sacred lands in the project vicinity on August 30, 2011. The NAHC responded on 
September 26, 2011. In its response, the NAHC stated that the sacred lands file records search 
did not indicate the presence of any known Native American cultural resources within one-half 
mile of the project area. In its transmittal, the NAHC enclosed a list of nine Native American 
individuals and/or organizations that might have knowledge of cultural resources in or near the 
project area. 
On October 4, 2011, TRC sent letters with a project location map to all individuals/groups on the 
list requesting information and comments. On October 5, 2011 Ms. Silvia Burley Chairperson of 
the California Valley Miwok Tribe responded that they have no issues in regards to the proposed 
project area and pipeline route. The Miwok requested being apprised of artifacts if found at this 
location. No other responses have been received as of this time. The NAHC correspondence can 
be found in Appendix E. 
The project area has not been the subject of any improvements/changes in the intervening time 
since the above stated consultations. Therefore, all information previously gathered regarding 
Native American cultural resources in the project vicinity, as outlined in the preceding 
paragraphs, is considered up to date and applicable to the proposed Endicott project. 
Local Regulations 
Stockton 2035 General Plan 
The City of StocktonÕs (City) primary objective is to assist in the continual identification of 
significant cultural resources to ensure their preservation and maintenance of the CityÕs heritage. 
The following goals and policies relating to cultural resources are applicable to the proposed 
Endicott project: 
Goal NCR-3 is to encourage the identification, protection, and enhancement of the CityÕs 
archaeological, historical, cultural, and paleontological resources for their cultural values. 
¥ NCR-3.5 Archaeological Resource Surveys: The City shall require that a record search, 
field surveys where appropriate, technical reports where appropriate be conducted for each 
project prior to approval. 
¥ NCR-3.6 Discovery of Archaeological Resources: Consistent with Stockton Municipal 
Code Chapter 16.36.050, in the event of archaeological/paleontological resources being 
discovered during excavation, the City shall require that construction work on the project 
area or pipeline route be suspended until a qualified archaeologist/paleontologist can access 
and make recommendations necessary to protect the resource. 
¥ NCR-3.7 Native American Resources: The City shall consult with Native American 
representatives regarding cultural resources. Coordination with the NAHC should begin at 
the onset of a particular project. 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-74 
¥ NCR-3.8 Discovery of Human Remains: Consistent with Stockton Municipal Code 
Chapter 16.36.050-Cultural Resources and CEQA Guidelines (Section 15064.5), if human 
remains of Native American origin are discovered during project construction, the City shall 
require compliance with all State laws relating to the disposition of Native American burials. 
The burials would fall within the jurisdiction of the NAHC. 
6.5.2. Methodology 
6.5.2.1. Archival Research Methods 
The California Historic Resources Information System maintains regional offices that manage 
site records for known cultural resource locations and related technical studies. The regional 
office for San Joaquin is the Central California Information Center at California State University, 
Stanislaus. Information regarding cultural resource studies and archaeological sites was compiled 
using a 1-mile radius around the project area. Sources reviewed include all known and recorded 
archaeological and historic sites and cultural resource reports. Additional resources that were 
consulted for relevant information included the California Register, National Register, California 
Inventory of Historic Resources, and California Points of Historical Interest, California 
Historical Landmarks, and historic maps. 
6.5.3. Environmental Setting 
The Proposed Endicott project is located on the eastern edge of the Sacramento-San Joaquin 
River delta and lies within the Great Central Valley. 
6.5.3.1. Prehistory 
Little is known of the earliest occupants of the Delta region, due to the meandering and rapid 
erosional patterns of the San Joaquin and Sacramento Rivers. There are several proposed 
sequences of cultural patterns (Fredrickson, 1974; Moratto, 1984; Ragir, 1972). The sequence 
utilized here is very broad and includes the Lower, Middle, and Late Archaic periods, and the 
Emergent Occupation. 
Lower Archaic (8000 to 3500 calibrated years before present (cal BP)) A generalized pattern of 
a mobile forager is characterized by the portable millingstones, which are large wide-stemmed 
projectile points. Archaeobotanical remains suggest an economy focused on acorns. 
Middle Archaic (3500 to 500 cal BP) During the Middle Archaic there appears to be an increase 
in regional trade and possibly signs of sedentism. The first cut shell beads appear in mortuaries. 
Mortars and pestles are documented shortly after 4000 cal BP Net sinkers are a typical marker 
for this time. The burial complexes with ornamental grave associations seem to represent a 
movement from forager to semi-sedentary land use (Jones and Klar, 2007). 
Upper Archaic (500 cal BP to cal Anno Domini (AD) 1050) The Upper Archaic period shows 
continued specialization and an increase in the complexity of technology. Acorns and fish were 
the predominant food sources. New bone tools and ornaments appear, including whistles, and 
barbless fish spears. Beads become very prominent with several types. Mortars and pestles 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-75 
continue to be the sole grinding tools. Net sinkers disappear at most sites. Mortuary practices 
change from a flexed position to an extended position. 
Emergent (cal A.D. 1050 to Historic) Many archaeologists believe that craft specialization, 
political complexity, and social ranking were highly developed. New bead types and 
multiperforated and bar-scored ornaments appear. The bow and arrow replace the dart and atlatl 
as the favored hunting tools (Moratto, 1984). The cultural traditions seem to be very similar to 
the ones witnessed at the time of the European contact. 
6.5.3.2. Ethnography 
The project area lies within the former territory of the Northern Valley Yokuts group known as 
the Yatchicumne. The Yokuts are unusual as they were one of the few California groups that 
lived in true tribes with distinct territories, and dialects. The territory of the Northern Valley 
Yokuts extended from the Diablo Range in the west to the Sierra Nevada foothills in the east, 
with the San Joaquin River as the core area (Wallace, 1978). Ethnographic literature on the 
Northern Valley Yokuts is lacking in depth predominantly due to the fact that the Northern 
Valley Yokuts were displaced so early. In 1830-1833 a malaria outbreak wiped out entire tribes. 
Ethnographical evidence indicates that villages were commonly situated near waterways or 
rivers, with a dependency on the natural resources of the marshes and sloughs. 
6.5.3.3. Historic Period 
The project area is within the vicinity of the industrial town of Stockton. The town was built 
around the shipping industry. The river's deep-water channel was completed in 1933 to make the 
Stockton Port District a supply depot for military operations in the Pacific. In 1944, the Navy 
built a supply depot at Rough and Ready Island which is directly across the San Joaquin River 
from the project area. From 1945 to 1956, the island was dominated by buildings and 
warehouses. The base is now decommissioned and Rough and Ready Island is currently 
controlled by the Stockton Port District. 
The Stockton Port District lies on the banks of the San Joaquin River about 65 kilometers (40 
miles) south of the Port of West Sacramento and about 96 kilometers (59 miles) east of the Port 
of San Francisco in central California. When irrigation was introduced and the Central Pacific 
Railroad arrived in 1869, the Stockton Port District grew as a market for farm produce and 
wines. While the Stockton Port District continues to be an important center for agricultural 
production of fruits, vegetables, and wines, it has also grown as a commercial and industrial 
center for the area. 
6.5.3.4. Paleontology 
On September 16, 2011 an online locality record search was conducted for the proposed project 
on the University of California, Museum of Paleontology website (University of California, 
2011). No localities were found within the proposed project area for invertebrates, microfossils, 
or vertebrates. The geologic map of the area was checked for the geologic rock units for the 
proposed project area (Wagner et al., 1991). The map shows that the proposed project area is 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-76 
underlined by the Dos Palos Alluvium dating from the late Pleistocene to early Holocene. This 
formation is predominantly flood basin deposits with low probability of fossils. 
6.5.3.5. Summary of Known Cultural Resources and Significant Findings 
An archival record search of the proposed project area was conducted by the Central California 
Information Center at California State University, Stanislaus on March 15, 2010. The records 
search was conducted to determine the extent, if any, to which the proposed project area had 
been previously surveyed, and the number and type of cultural resources in the area and within 
the project limits. The archival search consisted of an archaeological and historical records and 
literature review for an area within a one-mile radius of the proposed project. This record search 
provided background on the types of sites expected in the region, and covered the proposed 
project area. 
The record search results identified no resources within the proposed project area. There is one 
prehistoric resource (39-000237), a village site, approximately 1 mile away from the proposed 
project area. Thirty six plus historic resources, were located within a 1-mile radius of the project 
area, most of these resources were located on Rough & Ready Island in a historic district. Of 
these historic resources, the closest findings are two bridges: Burlington Northern Santa Fe 
Railway Bridge, which crosses over Navy Drive and has been classified as not eligible for the 
National Register; and a vehicular bridge located at the San Joaquin River at Navy Drive, which 
leads to Rough & Ready Island and was found eligible as a contributing element to the historic 
district Naval Supply Annex Historic District on Rough and Ready Island. The Navy Drive 
bridge is scheduled for replacement in 2015. Both bridges would not be impacted by the 
proposed project. Some of the other historic resources found within the 1-mile radius were levee 
segments, a segment of Daggett Road, ditch along Daggett Road, and a variety of structures and 
buildings on Rough & Ready Island. 
6.5.4. Standards of Significance 
CEQA guidelines Section 15064.5 defines historical resources as: 
¥ A resource listed in, or determined to be eligible by the State Historical Resources 
Commission, for listing in the California Register of Historical Resources; 
¥ A resource included in a local register of historical resources, as defined in section 5020.1(k) 
of the Public Resources Code or identified as significant in an historical resource survey 
meeting the requirements section 5024.1(g) of the Public Resources Code, shall be presumed 
to be historically or culturally significant. Public agencies must treat any such resource as 
significant unless the preponderance of evidence demonstrates that it is not historically or 
culturally significant; or 
¥ Any object, building, structure, site, area, place, record, or manuscript which a lead agency 
determines to be historically significant or significant in the architectural, engineering, 
scientific, economic, agricultural, educational, social, political, military, or cultural annals of 
California may be considered to be an historical resource, provided the lead agency's 
determination is supported by substantial evidence in light of the whole record. Generally, a 
resource shall be considered by the lead agency to be "historically significant" if the resource 
meets the criteria for listing on the California Register of Historical Resources. 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-77 
Determination of the significance of impacts to archaeological resources was made in accordance 
with Section 15064.5 of CEQA which indicates that the projectÕs impact to cultural resources 
would be considered significant if it would: 
¥ Cause a substantial adverse change in the significance of a historical resource; 
¥ Cause a substantial adverse change in the significance of unique archaeological resource; 
¥ Directly or indirectly destroy a unique paleontological resource or site or unique geologic 
feature; and/or 
¥ Disturb any human remains, including those interred outside of formal cemeteries. 
6.5.5. Impacts and Mitigation Measures 
Review of Cultural Resources Records uncovered no evidence of any significant cultural 
resources within the proposed project area. The proposed Endicott project would not affect 
known archaeological or historic resources of significance. There is a possibility that 
undocumented subterranean remains may be encountered during the course of project 
construction. If resources are encountered during construction, adverse impacts could be 
substantial, depending on the significance of the cultural resource. With the implementation of 
the following mitigation measure, no impacts are anticipated for the proposed Endicott project. 
ARCH-1 In the event that unanticipated archaeological resources should be accidentally 
discovered during project construction, a qualified archaeologist or paleontologist 
will be retained for evaluation of the find. If the find is determined to be a 
historical or unique archaeological resource, appropriate mitigation or avoidance 
measures will be taken in accordance with CEQA Guidelines 15064.5(f). During 
mitigation of unanticipated archaeological resources, it would not be necessary for 
work to halt in construction areas not affected by such finds. Any historically 
significant cultural materials discovered during project construction will be the 
subject of professional scientific analysis and a report to be prepared by a qualified 
archaeologist. In the event that such a discovery should contain human remains, the 
following steps shall be taken as outlined in CEQA Guidelines 15064.5 (e)(1): 
(1) There shall be no further excavation or disturbance of the site or any nearby 
area reasonably suspected to overlie adjacent human remains until: 
(A) The coroner of the county in which the remains are discovered must be 
contacted to determine that no investigation of the cause of death is 
required, and 
(B) If the coroner determines the remains to be Native American: 
1. The coroner shall contact the Native American Heritage Commission 
within 24 hours. 
2. The Native American Heritage Commission shall identify the person or 
persons it believes to be the most likely descended from the deceased 
Native American. 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-78 
3. The most likely descendent may make recommendations to the 
landowner or the person responsible for the excavation work, for means 
of treating or disposing of, with appropriate dignity, the human remains 
and any associated grave goods as provided in Public Resources Code 
Section 5097.98 or 
(2) Where the following conditions occur, the landowner or his authorized 
representative shall rebury the Native American human remains and associated 
grave goods with appropriate dignity on the property in a location not subject to 
further subsurface disturbance. 
(A) The Native American Heritage Commission is unable to identify a most 
likely descendent or the most likely descendent failed to make a 
recommendation within 24 hours after being notified by the commission. 
(B) The Descendant identified fails to make a recommendation; or 
(C) The landowner or his authorized representative rejects the recommendation 
of the descendant, and the mediation by the Native American Heritage 
Commission fails to provide measures acceptable to the landowner. 
6.5.6. Cultural Resources Initial Study Responses 
Table 3.5-1: Cultural Resources Initial Study Responses 
WOULD THE PROJECT: 
Potentially 
Significant 
Impact 
Less Than 
Significant 
Impact with 
Mitigation 
Incorporated 
Less Than 
Significant 
Impact 
No 
Impact 
a) Cause a substantial adverse change in the 
significance of a historical resource as 
defined in ¤15064.5? 
. . . . 
b) Cause a substantial adverse change in the 
significance of an archaeological resource 
pursuant to ¤ 15064.5? 
. . . . 
c) Directly or indirectly destroy a unique 
paleontological resource or site or unique 
geologic feature? 
. . . . 
d) Disturb any human remains, including those 
interred outside of formal cemeteries? 
. . . . 
6.5.7. Response to Questions 
6.5.7.1. Historical Resource: No Impact 
The Port, including the proposed Endicott project lease area, is not listed in the National Register 
of Historic Places, California Register of Historic Resources, California Inventory of Historic 

6.5 Cultural Resources 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-79 
Resources, California Historical Landmarks, Survey of Surveys, or California Points of 
Historical Interest (National Park Service, 2013). A record search revealed that the lease area 
has never been the subject of major improvements including permanent structures. The two 
closest possible historic resources to the proposed Endicott project are bridges across the San 
Joaquin River. However, neither bridge will be affected by the proposed Endicott project. 
Additionally, the Stockton Port District (lead agency) has not determined any object, building, 
structure, site, or area of the project area to be historically significant. Therefore, the proposed 
improvements and operations would not cause any substantial adverse change in the significance 
of a historical resource as identified by the lead agency, in accordance with CEQA guidelines 
Section 15064.5. 
6.5.7.2. Archaeological Resource: Less than Significant 
A cultural resource records search completed at the Central California Information Center 
indicated that there were no cultural resources recorded within the proposed Endicott project 
area. Although no evidence of any archaeological features are known within the proposed 
project area, there is still a possibility that undocumented finds may be encountered. 
Additionally, the NAHC was contacted and their records were searched for known cultural 
resources recorded within the proposed Endicott project area; and letters were sent to Native 
American individuals and organizations that may have knowledge of cultural resources in the 
proposed project area. No known cultural resources were recorded within the proposed Endicott 
project area. As such, it is highly unlikely that cultural resources will pose a potential issue. 
6.5.7.3. Paleontological Resource: Less than Significant 
A search of geologic maps of the area shows that the proposed Endicott project is underlined by 
the Dos Palos Alluvium dating from the late Pleistocene to early Holocene. This formation is 
predominantly flood basin deposits with low probability of containing fossils. Although unlikely, 
there is potential for unknown paleontological resources to be impacted as a result of the 
proposed Endicott project activities. With the implementation of mitigation measures, discussed 
above, and the low likelihood for the existing formation to contain fossils or other sensitive 
cultural resources, impacts to paleontological resources are considered less than significant. 
6.5.7.4. Human Remains: Less than Significant 
The cultural resources records search concluded that no evidence of any known human remains 
was located within the proposed project area. Due to the buried nature of such finds, and the 
uncertainty of whether or not any significant cultural resource exists, it is not feasible to conduct 
extensive studies prior to implementation of the proposed project. 
Research showed that there are no known archaeological sites or cemeteries with human remains 
within a 1-mile radius of the lease area. Nevertheless, while the likelihood of finding human 
remains is small, there is potential that unidentified human remains could be found within or 
nearby the lease area. With the implementation of the mitigation measures, discussed above, any 
potential impacts would be considered negligible. Therefore, construction of the proposed 
Endicott project would not disturb any human remains, including those interred outside of formal 
cemeteries. Project-related impacts to human remains would be less than significant. 

6.6 Geology 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-80 
6.6 Geology, Soils, and Seismicity 
This section contains a description of the setting regarding geology, soils, and seismicity in the 
proposed lease area, along with a description of the existing regional physiography, geologic 
hazards, and soil characteristics in the area. The following discussion is based primarily on the 
following information sources, and other publicly available geologic literature: 
¥ United States Geological Survey (USGS) topographic and geologic maps; 
¥ Geotechnical Investigation, Endicott Biofuel, LLC Stockton Project, prepared for the 
proposed Endicott project by TRC Solutions Inc. (TRC) October, 2013 (TRC Geotechnical 
Investigation). 
6.6.1. Background 
6.6.1.1. Regulatory Context 
Title 24 Uniform Building Code sets building construction standards for safety and protection in 
the event of ground shaking. 
6.6.2. Methodology 
Information on geologic, soil, mineral resource, and paleontological resource conditions in the 
proposed project area was compiled from existing literature, maps, and data, including research 
and analysis documented in the TRC Geotechnical Investigation (Appendix G) following the 
standards outlined in Title 24 of the Uniform building code. 
6.6.3. Environmental Setting 
6.6.3.1. Geologic Setting 
The proposed project is located within a region known as the Great Valley geomorphic province 
(Great Valley). The Great Valley consists of alluvial plains, approximately 50 miles wide and 
400 miles long, in the central part of California. The Great Valley is a trough in which sediments 
have been deposited almost continuously since the Jurassic Period (approximately 160 million 
years ago). It is drained by the Sacramento and San Joaquin Rivers, which drain into the San 
Francisco Bay (California Department of Conservation, 2002). 
The proposed project area is situated within the San Joaquin Valley, immediately adjacent to the 
east side of the San Joaquin River, and is underlain by the Quaternary-aged Dos Palos Alluvium, 
which is described as floodplain deposits. Floodplain deposits in the area can be as thick as 
approximately 1,400 feet deep. The depth to bedrock in the lease area is anticipated to be 
approximately 200 feet. 
6.6.3.2. Topography Setting 
The TRC Geotechnical Investigation described the lease area as relatively level and gently 
sloping to the north with less than 5 feet of topographic relief. The lease area is nearly level in 

6.6 Geology 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-81 
elevation with the surrounding area. Limited topographic relief is found on the western side of 
the lease area and is due to stock piles of dirt from other projects within the Port. The San 
Joaquin River levee is immediately north of the lease area. Elevation changes to the public 
ROW to be utilized for the product and feedstock pipeline are extremely limited as the pipelines 
are aligned within Port roads. 
6.6.3.3. Soils 
According to the Soil Survey of San Joaquin County, Yellowlark Gravelly Loam is mapped 
throughout the entire lease area (See Figure 6.6-1: Soil Survey). Yellowlark Gravelly Loam 
consists of moderately well drained soil that formed in alluvium derived from mixed rock 
sources. Yellowlark soils are on intermediate fan terraces and stream terraces. The slope is 2 to 5 
percent. The mean annual precipitation is about 17 inches and the mean annual temperature is 
about 60 degrees F. 
6.6.3.4. Geologic Hazards 
Earthquakes 
The lease area is not located within a currently designated Alquist-Priolo Earthquake Fault Zone 
(formerly known as a Special Studies Zone). No known surface expression of active faults is 
believed to cross the lease area. Fault rupture through the lease area is therefore not anticipated 
(TRC, 2013) (See Figure 6.6-2: Fault Map). 
The nearest active fault is the Greenville Fault, located approximated 21 miles southwest of the 
lease area. The Maximum Moment magnitude of the maximum probable earthquake on the 
Greenville Fault is estimated to be 6.0. Other nearby faults exhibiting historical activity, within 
the past 2000 years are the Concord-Green Valley and Hayward faults. 

6.6 Geology 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-84 
Seismic Ground Shaking 
A qualitative evaluation of geologic hazards, made by TRC as part of their geotechnical 
investigation, indicated a peak ground surface acceleration of 0.30 g-force (g), which is equal to 
SDS/2.5 as discussed in Item 23 of the California Geological Survey Note 48 (TRC, 2013). 
Liquefaction 
Liquefaction is a seismic phenomenon in which loose, saturated, fine-grained granular soils 
behave similar to a fluid when subjected to high-intensity ground shaking. An increase in pore 
pressure occurs as the soil attempts to compact in response to the shaking, resulting in less grainto-
grain solid contact, and therefore loss of strength. Liquefaction occurs when three general 
conditions exist: shallow groundwater (i.e., 40 feet below ground surface or less); low density, 
fine-grained sandy soils; and high-intensity ground motion. Effects of liquefaction on level 
ground can include sand boils, settlement, and bearing capacity failures below structure 
foundations. 
Explorations and analysis performed by TRC concluded that, in general, there appears to be a 
fairly consistent liquefiable layer across the lease area. Differential settlement from liquefaction 
for shallow foundations and site improvements were estimated to be approximately 1 inch in the 
upper 50 feet (TRC, 2013) 
Lateral Spreading 
Lateral spreading typically occurs as a form of horizontal displacement of relatively flat-lying 
alluvial material toward an open or ÒfreeÓ face such as an open body of water, channel, or 
excavation. In soils, this movement is generally due to failure along a weak plane, and may often 
be associated with liquefaction. The San Joaquin River runs to the north of the lease area. 
However, the River is approximately 70 feet from the lease area boundary and the shallow 
liquefiable layers are not consistent throughout the lease area. Therefore, the probability of 
lateral spreading occurring at the lease area during a seismic event is relatively low (TRC, 2013). 
6.6.4. Standards of Significance 
An impact to geology, soils, and seismicity would be considered significant if the project would: 
¥ Expose people or structures to potential substantial adverse effects, including the risk of loss, 
injury, or death involving: 
Ð rupture of a known earthquake fault, as delineated on the most recent Alquist-Priolo 
Earthquake Fault Zoning Map issued by the State Geologist for the area or based on other 
substantial evidence of a known fault; 
Ð strong seismic ground shaking; 
Ð seismic-related ground failure, including liquefaction; 
Ð landslides; and/or 

6.6 Geology 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-85 
Ð subsidence; 
¥ Result in substantial soil erosion, siltation, changes in topography, the loss of topsoil or 
unstable soil conditions from excavation, grading or fill; 
¥ Be located on a geologic unit or soil that is unstable, or that would become unstable as a 
result of the project, and potentially result in on- or off-site landslide, lateral spreading, 
subsidence, liquefaction, or collapse; 
¥ Be located on expansive soil, as defined in Table 18-1-B of the Uniform Building Code 
(1994), creating substantial risks to life or property; and/or 
¥ Have soils incapable of adequately supporting the use of septic tanks or alternative 
wastewater disposal systems where sewers are not available for the disposal of wastewater. 
6.6.5. Impacts and Mitigation Measures 
The proposed project would be constructed to meet the safety standards listed in the Uniform 
Building Code. Best Management Practices (BMPs) for control of erosion would be executed on 
site as outlined in the Stormwater Pollution Prevention Plan (SWPPP) prepared for the City of 
Stockton and Stockton Port District. Grading and erosion control plans would be prepared in 
accordance with the CityÕs engineer requirements for improvement plans. A detailed 
geotechnical survey was completed and grading, soil compaction, and structural design would be 
implemented in accordance with the recommendations of the geotechnical report (see Appendix 
G: Geotechnical Report). No significant impacts are anticipated. 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-86 
6.6.6. Geology, Soils, and Seismicity Initial Study Responses 
Table 6.6-1: Geology, Soils, and Seismicity Initial Study Responses 
WOULD THE PROJECT: 
Potentially 
Significant 
Impact 
Less Than 
Significant 
Impact with 
Mitigation 
Incorporated 
Less Than 
Significant 
Impact 
No 
Impact 
a) Expose people or structures to potential 
substantial adverse effects, including the 
risk of loss, injury, or death involving: 
. . . . 
i) Rupture of a known earthquake fault, 
as delineated on the most recent 
Alquist-Priolo Earthquake Fault Zoning 
Map issued by the State Geologist for 
the area or based on other substantial 
evidence of a known fault? Refer to 
Division of Mines and Geology Special 
Publication 42. 
. . . . 
ii) Strong seismic ground shaking? . . . . 
iii) Seismic-related ground failure, 
including liquefaction? 
. . . . 
iv) Landslides? . . . . 
b) Result in substantial soil erosion or the loss 
of topsoil? 
. . . . 
c) Be located on a geologic unit or soil that is 
unstable, or that would become unstable as 
a result of the project, and potentially result 
in on- or off-site landslide, lateral spreading, 
subsidence, liquefaction, or collapse? 
. . . . 
d) Be located on expansive soil, as defined in 
Table 18-1-B of the Uniform Building Code 
(1994), creating substantial risks to life or 
property? 
. . . . 
e) Have soils incapable of adequately 
supporting the use of septic tanks or 
alternative wastewater disposal systems 
where sewers are not available for the 
disposal of wastewater? 
. . . . 

6.6 Geology 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-87 
6.6.7. Responses to Initial Study Questions 
6.6.7.1. Exposed People to Potential Substantial Adverse Effects: Less than Significant 
It is highly improbable that the proposed Endicott project would be the cause of loss of life or 
other injury from risks associated with geologic and soil factors of the proposed project. The 
improvements of the proposed Endicott project will be constructed in accordance with local, 
State, and National regulations (as will be discussed in ensuing sections of the document). 
Included in these regulations in the CBC (Chapter 16) which provides specific seismic 
regulations; Chapter 16, as discussed below, addresses methods to reduce seismically related 
risks to acceptable levels. The proposed Endicott project will be constructed to these standards, 
and as such, will result in less than significant level related to exposure to loss of life and/or 
injury. 
6.6.7.2. Alquist-Priolo Earthquake Faults: No Impact 
The nearest active fault is the Greenville Fault, located approximately 21 miles southwest of the 
lease area. The lease area is not located within a currently designated Alquist-Priolo Earthquake 
Fault Zone and no known surface expression of active faults is believed to cross the lease area; 
therefore, fault rupture through the lease area is not anticipated (TRC, 2013). There would be No 
Impact. 
6.6.7.3. Ground Shaking: Less than Significant 
The Greenville Fault, located approximately 21 miles southwest of the lease area, has historically 
produced a peak ground acceleration of 0.15g in Brentwood, approximately 30 miles west of the 
lease area. According to the TRC Geotechnical Investigation, current practice indicates a peak 
ground surface acceleration of 0.30g to be expected to occur at the lease area. The proposed 
Endicott project would be constructed to meet the safety standards established by Uniform 
Building Code and the API Standards for Petroleum Storage Tanks (API Standards). The 
feedstock and FAME/B100 pipeline would be constructed to appropriate API, ASME, and NFPA 
standards. Adherence to applicable seismic standards requirements reduces this impact to a lessthan-
significant level. 
6.6.7.4. Liquefaction: Less than Significant 
All structures would be designed to withstand strong ground motion and ground failure 
(liquefaction) resulting from a design earthquake in accordance to the adopted API standards. 
The TRC Geotechnical Investigation indicates that some of the sand and silt layers encountered 
may theoretically liquefy and result in post-seismic total and differential settlement. The TRC 
Geotechnical Investigation recommends structures on the lease area be supported on deep 
foundations consisting of driven, precast, pre-stressed concrete friction piles or augured cast-inplace 
piles. The Geotechnical Investigation further stated that the above ground portion of the 
pipeline would require support by steel supports that meet the CBC standards and that the prior 
to the final placement of any buried pipeline, the consultation of a corrosion engineer would be 
required. Such measures would ensure adequate protection of the pipeline (both against 
corrosion and for means of support). Endicott would incorporate the recommended project 
design specifications outlined in the TRC Geotechnical Investigation; therefore, no additional

6.6 Geology 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-88 
project specific mitigation measures are proposed and impacts resulting from liquefaction are 
anticipated to be less than significant. 
6.6.7.5. Landslides: No Impact 
The lease area and pipeline route and are relatively level and gently sloping to the north with 
limited topographic relief (TRC, 2013) furthermore, the proposed pipeline will be buried in the 
existing public ROW, and will be placed upon compacted soils (per the Geotechnical Report). 
Where buried, upon completion of excavation efforts for pipeline placement, the surrounding 
ground will be leveled to ensure that no landslides will occur from any soil disturbance. TRCÕs 
Geotechnical Investigation did not identify any potential project impacts from landslides. The 
lack of significant slopes on or near the Port indicates that the hazard from slope instability, both 
landslides and debris flows, is negligible. Therefore, no impacts resulting from landslides are 
anticipated. 
6.6.7.6. Subsidence: Less than Significant 
Some of the sand and silt layers at the proposed lease area may theoretically liquefy and result in 
post-seismic total and differential settlement. TRCÕs Geotechnical Investigation have included 
the provision of design parameters, such as foundations, to resist or accommodate post-seismic 
total and differential settlement; therefore, this impact would be less than significant and no 
project specific mitigation measures are required. 
6.6.7.7. Soil Erosion: Less than Significant 
Since the proposed lease area is relatively flat, the potential for substantial soil erosion is 
considered minimal. BMPs for control of erosion would be implemented as part of the CityÕs 
grading and building permits to reduce erosion of soils on the proposed lease area. BMPs would 
be implemented as part of the encroachment permits for the pipeline installation within public 
right-of-ways, which would mitigate potential impacts on soil erosion as a result of construction. 
Such BMPs could include, but is not limited to: the utilization of a sediment trap for all drains, 
straw bale barriers, the placement of mulch (straw or hydraulic) throughout the property, and the 
placement of geotextile mats for any of the sloped areas. In addition, the requirements of the 
State General Construction Stormwater Permit for projects would provide further review, 
monitoring, and mitigation as required by the State Regional Water Quality Control Board, 
which would ensure that this impact would be less than significant. 
6.6.7.8. Unstable Soils: Less than Significant 
It has been suggested that several of the soil layers beneath the highest anticipated level of 
groundwater (9 feet below grade) would be expected to liquefy or experience liquefaction 
induced settlement from a maximum credible earthquake (MCE) magnitude of 6.8. All grading 
would be performed in accordance with the recommended grading specifications contained in the 
City of Stockton Grading Regulations, which would reduce any potential impacts to a less than 
significant level. 

6.6 Geology 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-89 
The TRC Geotechnical Investigation indicates that some of the sand and silt layers encountered 
may theoretically liquefy and result in post-seismic total and differential settlement. Therefore, 
foundations would be designed to resist or accommodate this settlement. By performing 
measures incorporated in the Geotechnical Report, the proposed Endicott project will ensure that 
foundations for the proposed structures are adequate for the desired purposes, thereby resulting 
in less than significant impacts. 
6.6.7.9. Expansive Soils: Less than Significant 
The lease area does not contain expansive soils which exhibit expansion related hazards. 
However, TRCÕs Geotechnical Investigation did indicate that surficial soils of the lease area are 
moderately expansive. As recommended in the TRC Geotechnical Investigation, the buildingÕs 
slab-on-grade and exterior concrete flatwork would be supported on a layer of non-expansive 
fill; therefore, no additional-project specific mitigation measures are proposed and the resulting 
impacts would be less than significant. 
6.6.7.10. Septic Tanks and Wastewater Disposal System: No Impact 
TRCÕs Geotechnical Investigation did not identify that soils would be incapable of adequately 
supporting the use of septic tanks or alternative waste disposal systems where sewers are not 
available for the disposal of wastewater. No in-ground sewage disposal is proposed. Therefore, 
no impacts are anticipated. 

6.7 Greenhouse Gas Emissions 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-91 
6.7.1.2. Federal Regulations 
In October 2009, EPA issued a Final Rule for mandatory reporting of GHG emissions. This Final 
Rule applies to fossil fuel suppliers, industrial gas suppliers, direct GHG emitters, and 
manufactures of heavy-duty and off-road vehicles and vehicle engines, and requires annual 
reporting of emissions. The Final Rule went into effect on December 29, 2009, with data 
collection between January 1, 2010, and March 2011. This rule does not regulate the emission of 
GHGs, it only requires the monitoring and reporting of GHG emissions for sources above 
specific thresholds. Additional legislative measures have been taken to attempt to regulate 
GHGs, in other manners, however; each has failed in the process (the most recent attempt was in 
the American Clean Energy and Security Act of 2009 (Waxman-Markey Bill) which had success 
in the House of Representatives, but failed to receive necessary support in the Senate. 
6.7.1.3. State Regulations 
AB 32 requires California to reach 2000 levels of greenhouse gas (GHG) emissions by 2010, 
reach 1990 levels by 2020, and have 80 percent less emissions than 1990 levels by 2050. CARB, 
together with the California Energy Commission and other agencies, has been developing and 
revising the regulation, and as of January 1, 2012 the new policies have gone into effect and are 
legally enforceable. 
The pollutants regulated by either the CAA or CCAA are known as criteria pollutants. Noncriteria 
air pollutants are not regulated by these Acts, but are of concern as they may be 
precursors to criteria air pollutants, or could also have other adverse impacts. Criteria pollutants 
include particulate matter, ozone (O3), NOx, CO, SO2, and lead (Pb). Further detailed description 
of these pollutants is provided in section 6.3.3.2, Air Quality Pollutants, which follows. 
Important non-criteria pollutants include GHG emissions and air toxics. GHGs are produced 
from electricity generation, road transportation, and other energy sources; industrial processes; 
agriculture, forestry, and other land use; solid waste disposal; and wastewater treatment and 
discharge. Air toxics are generated from industrial processes (e.g., gas stations, dry cleaners, or 
car repairs), as well as mobile sources using diesel engines and agricultural sources. 
Despite a clearly established timeline for AB 32 implementation, the California Attorney 
GeneralÕs office has made the claim that CEQA requires that any projects currently in the 
process of CEQA approval must immediately satisfy the goals of AB 32 and the GovernorÕs 
Executive Order 2-3-05. The Courts have upheld several challenges to the consideration of 
GHGs under the auspice of CEQA. As a result, any project receiving CEQA approval is required 
to calculate pre-project and post-project, GHG emissions to identify and characterize the 
projectÕs carbon emissions. 
6.7.1.4. Local Regulations 
The SJVAPCD adopted the Climate Change Action Plan (CCAP) in August 2008 to assist lead 
agencies in assessing and reducing the impacts of project specific GHG emissions on global 
climate change. The CCAP relies on the use of performance based standards, otherwise known 
as Best Performance Standards (BPS) to assess significance of project specific greenhouse gas 
emissions on global climate change. Projects implementing BPS are determined to have a less 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-92 
than significant impact. Otherwise, demonstration of a 29 percent reduction in GHG emissions, 
from business-as-usual, is required to classify a projectÕs impact as less than significant. 
6.7.2. Methodology 
A qualitative assessment of the GHG emissions resulting from the proposed project was 
previously discussed in Section 6.3 and it was determined that there would be no significant 
impacts resulting from the construction and operation of the proposed project. (See Section 6.3) 
6.7.3. Environmental Setting 
The environmental setting was previously discussed in detail in the air quality section (See: 
Section 6.3). Greenhouse gasses and various forms thereof were defined and described. To 
avoid duplicative discussions, please refer to Section 6.3. 
6.7.4. Standards of Significance 
GHG emissions of the proposed Endicott project would be considered significant should the 
following factors be demonstrated: 
¥ Generate greenhouse gas emissions. either directly or indirectly, that may have a significant 
impact on the environment; and 
¥ Conflict with an applicable plan, policy or regulations adopted for the purpose of reducing 
the emissions of greenhouse gasses. 
6.7.5. Impacts and Mitigation Measures 
6.7.5.1. Endicott Stockton GHG-specific Impacts 
No specific mitigation measures will be required for the GHG emissions of the proposed 
Endicott project. Mitigation measures previously discussed in the air quality section will be 
applicable to the limitation of GHGs. In particular, these measures include: 
AQ-4: Use alternative fuel or catalyst-equipped diesel construction equipment; 
AQ-5: Minimize idling time (e.g., 5-minute maximum) 
AQ-6: Replace fossil-fueled equipment with electrically driven equivalents when possible; 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-93 
6.7.6. Green House Gas Initial Study Responses 
Table 3.7-1 Green House Gas Initial Study Responses 
WOULD THE PROJECT: 
Potentially 
Significant 
Impact 
Less Than 
Significant 
Impact with 
Mitigation 
Incorporated 
Less Than 
Significant 
Impact 
No 
Impact 
a) Generate greenhouse gas 
emissions, either directly or 
indirectly, that may have a 
significant impact on the 
environment? 
. . . 
. 
b) Conflict with an applicable plan, 
policy or regulations adopted for 
the purpose of reducing the 
emissions of greenhouse gasses? 
. . . 
. 
6.7.7. Response to Initial Study Questions 
6.7.7.1. Generate Green House Gas Emissions: Less Than Significant Impact with 
Mitigation Incorporated 
The proposed Endicott project would be designed and operated in accordance with the 
SJVAPCDÕs Best Performance Standards (BPS). The proposed project is therefore deemed to 
represent a less than significant impact as established by the SJVAPCDÕs Climate Change 
Action Plan (CCAP). Additionally, while GHGs will likely be emitted throughout the 
construction phase (through the utilization of heavy duty construction equipment), the 
construction methods will be temporary and will not cause a significant increase in GHG 
emissions (See: Section 6.3 for detailed analysis). Additional mitigation measures will be 
employed throughout the construction phase to ensure that air pollution emitted from the 
construction equipment is limited. As such, the impact on GHG emissions from both the 
construction and operation of the proposed Endicott project is less than significant with 
mitigation measures incorporated. 
6.7.7.2. Conflict with an Applicable Plan Adopted to Reduce Green House Gas 
Emissions: No Impact. 
The proposed Endicott project will be consistent with SJVAPCD guidance as outline in their 
CCAP. The primary concern of the CCAP is to demonstrate the reduction of 29 percent in GHGs 
from a business-as-usual scenario. However, according to the CCAP, projects implementing BPS 
will be considered to have a less than significant impact. The proposed Endicott project will 
follow BPS guidelines as defined by the SJVAPCDÕs CCAP for all boilers, steam generators and 
other applicable equipment. Considering the implementation of these measures, there will be No 
Impact to the local plan that has been adopted to reduce GHGs consistent with AB32. 

6.8 Hazardous Materials 
Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-94 
6.8 Hazards and Hazardous Materials 
This section contains a description of hazards and hazardous materials in the proposed project 
area as well as hazardous materials which may be found within the Port and within the region, 
generally. The discussion is based primarily on the Phase I Environmental Site Assessment 
prepared for the proposed project area in August of 2013 (Appendix F), and other available 
environmental hazard literature. These data sources were supplemented by observations made 
during site reconnaissance visits conducted on July 24, 2013. 
Hazards related to the proposed Endicott project primarily fall under two categories based on the 
origin of the hazard: (1) hazards created by project operations that impact facilities and/or people 
on the proposed project area or nearby and (2) hazards created by nearby uses that impact the 
facilities and/or people on or near the proposed project area. Exposure to hazardous chemicals 
could fall under both categories (hazardous chemicals could originate onsite or offsite), whereas 
risk to people and property on the proposed project area by proximity to airports would fall under 
the second category. 
6.8.1. Background 
6.8.1.1. Hazardous Substances Defined 
Hazardous materials can be defined as such based on various criteria, including toxicity, 
ignitability, corrosivity, or reactivity. The term Òhazardous materialÓ is defined as any material 
that, because of quantity, concentration, or physical or chemical characteristics, poses a 
significant present or potential hazard to human health and safety or to the environment. 
(California Code of Regulations (CCR) Title 22, Division 4.5 Chapter 10, Article 2, ¤66260.10). 
Once a hazardous material becomes ready for discard, it becomes a hazardous waste. A 
hazardous waste, for the purpose of this report, is any hazardous material that is abandoned, 
discarded, or (planned to be) recycled. In addition, hazardous wastes may occasionally be 
generated by actions that change the composition of previously non-hazardous materials. The 
same criteria: toxicity, ignitability, corrosivity, or reactivity that renders a material hazardous 
makes waste hazardous. (CCR Tit. 22, Div. 4.5 Ch. 10, Art. 3). 
6.8.1.2. Regulatory Context 
Numerous federal, state, and local agencies regulate the storage, use, transport, generation, or 
handling of these materials. The transfer, handling, storage, and transport of hazardous liquid 
bulk cargoes within the Port are governed by the San Joaquin County Environmental Health 
Department (SJCEHD). 
Federal Regulations 
Regulations Pertaining to Hazardous Substances 
Federal regulatory agencies include the United States Environmental Protection Agency (U.S. 
EPA), Occupational Safety Health Administration (Fed/OSHA), the United States Department of 

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Initial Study 6-95 
Transportation (DOT) and the National Institute of Health (NIH). The following represent some 
of the federal laws and guidelines governing hazardous substances: 
¥ Clean Air Act (CAA) (42 US Code Section 7401, et seq./40 CFR) 
¥ Occupational Safety and Health Act (29 US Code Sections 651, et seq./29 CFR) 
¥ Comprehensive Environmental Response Compensation and Liability Act (CERCLA) (42 
US Code Section 9601, et seq./29, 40 CFR) 
¥ Superfund Amendments and Reauthorization Act Title III (42 USC Section 11001, et 
seq./29, 40 CFR) 
¥ Resource Conservation and Recovery Act (RCRA) (42 US Code Section 6901, et seq./40 
CFR) 
¥ Safe Drinking Water Act (42 US Code Section 300f, et seq./40 CFR) 
¥ Toxic Substances Control Act (15 US Code Section 2601, et seq./40 CFR) 
¥ Hazardous Materials Transportation Act (49 U.S.C. 1801, et seq.) and regulations issued 
under that Act by the Department of Transportation 
¥ Pollution Prevention Act (42 US Code Section 13101, et seq./40 CFR) 
¥ Renewable Fuel Standard Program and RIN Generation registration (40 CFR 80.1126(e)(2). 
¥ Emergency Planning and Community Right-to-Know Act 40 CFR 355 
¥ Reporting Hazardous Chemical Storage Ð Tier II Reporting 
At the federal level, the principal agency regulating the generation, transport, and disposal of 
hazardous substances is the U.S. EPA, under the authority of RCRA. U.S. EPA regulates 
hazardous substance sites under CERCLA. Applicable federal regulations are contained 
primarily in Titles 29, 40, and 49 of the CFR. 
Hazardous Substances Worker Safety Requirements 
The Fed/OSHA is the agency responsible for ensuring worker safety. Fed/OSHA sets federal 
standards for implementation of training in the work place, exposure limits, and safety 
procedures in the handling of hazardous substances (as well as other hazards). Fed/OSHA also 
establishes criteria by which each state can implement its own health and safety program. 
Hazardous Materials Transportation 
The DOT regulates the interstate transport of hazardous materials and wastes through 
implementation of the Hazardous Materials Transportation Act. This Act specifies driver training 
requirements, load labeling procedures, and container design and safety specifications. 
Transporters of hazardous wastes must also meet the requirements of additional statutes such as 
RCRA. 

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Endicott Biofuel Production Facility Project November 2013 
Initial Study 6-96 
Hazardous Substances Handling Requirements 
RCRA established a federal hazardous substance Òcradle-to-graveÓ regulatory program that is 
administered by U.S. EPA. Under RCRA, U.S. EPA regulates the generation, transportation, 
treatment, storage and disposal of hazardous substances. RCRA was amended in 1984 by the 
Hazardous and Solid Waste Act (HSWA), which affirmed and extended the Òcradle-to-graveÓ 
and specifically prohibits the use of certain techniques for the disposal of certain hazardous 
substances. 
U.S. Environmental Protection Agency (EPA) 
The EPA is responsible for the National Contingency Plan and acts as the lead agency in 
response to an onshore spill. EPA also serves as co-chairman of the Regional Response Team, 
which is a team of agencies established to provide assistance and guidance to the on-scene 
coordinator (OSC) during the response to a spill. The EPA also regulates disposal of recovered 
oil and is responsible for developing regulations for Spill Prevention, Control, and 
Countermeasures (SPCC) Plans. SPCC Plans are required for non-transportation-related onshore 
and offshore facilities that have the potential to spill oil into waters of the U.S. or onto adjoining 
shorelines. The proposed Endicott project would be required to prepare and maintain a SPCC 
Plan. 
State Regulations 
Regulations Pertaining to Hazardous Substances 
The agency which has primary State jurisdiction to regulate and enforce hazardous materials 
regulations within the Port is SJCEHD. However, the Regional Water Quality Control Board 
(RWQCB) and the California Department of Toxic Substances Control (DTSC) have secondary 
jurisdiction, and in instances in which hazardous waste may cause air pollution, the SJVAPCD 
would also have jurisdiction. Lastly, both the federal and state Occupational Safety and Health 
Administration (Fed/OSHA and Cal/OSHA) in the preparation of hazardous materials 
remediation site safety plans intended to protect the health of construction and contamination 
remediation workers. 
The California Environmental Protection Agency (Cal/EPA) and the Office of Emergency 
Services (OES) establish rules governing the use of hazardous substances. The SWRCB has 
primary responsibility to protect water quality and supply. 
Cal/EPA was created in 1991 to better coordinate state environmental programs, reduce 
administrative duplication, and address the greatest environmental and health risks. Cal/EPA 
unifies the stateÕs environmental authority under a single accountable cabinet-level agency. The 
Secretary for Cal/EPA oversees the following agencies: Air Resources Board, Integrated Waste 
Management Board, Department of Pesticide Regulation, SWRCB, DTSC, and OES. 
Applicable State laws include the following: 
¥ California Accidental Release Prevention Law (California Health and Safety Code Section 
25531, et seq./19 CCR) 

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¥ California Fire Code (California Health and Safety Code Section 13000, et seq./19 CCR) 
¥ Uniform Fire Code (California Code of Regulation Section 1924(b), 3221, 6150, 6184) 
¥ Carpenter-Presley-Tanner Hazardous Substance Account Act ÒState SuperfundÓ (California 
Health and Safety Code Section 25300, et seq./California Revenue and Tax Code Section 
43001, et seq.) 
¥ California Building Code (California Health and Safety Code Section 18901, et seq./24 CCR) 
¥ Hazardous Waste Control Law (HWCL) (California Health and Safety Code Section 25100, 
et seq./22 CCR) 
¥ California Occupational Safety and Health Act (Cal/OSHA) (California Labor Code Section 
6300-6718/ 8 CCR) 
¥ Hazardous Materials Handling and Emergency Response ÒWaters BillÓ (California Health 
and Safety Code Section 25500, et seq./19 CCR) 
¥ Hazardous Substances Act (California Health and Safety Code Section 108100, et seq.) 
¥ Safe Drinking Water and Toxic Enforcement Act ÒProposition 65Ó (California Health and 
Safety Code Sections 25180.7, 25189.5, 25192, 25249.5-25249.13/8, 22 CCR) 
¥ California Air Quality Laws (California Health and Safety Code Section 39000, et seq./17 
CCR) 
¥ California Clean Air Act (California Health and Safety Code Section 44300, et seq./17 CCR) 
¥ Hazardous Substances Information and Training Act (Cal/OSHA) (Worker Right-to-Know 
Law) (California Labor Code Section 6360, et seq.) 
¥ Hazardous Substances Release Response Plans and Inventory Act 
¥ Air Toxics ÒHot SpotsÓ Information and Assessment Act of 1987 (A.B. 2588) (California 
Health and Safety Code Section 44300, et seq.) (17 California Code of Regulations Section 
90700, et seq.) 
Hazardous Substances Handling Requirements 
Within the Cal/EPA, DTSC has primary regulatory responsibility, with delegation of 
enforcement to disposal of hazardous substances under the authority of the HWCL. Regulations 
implement the HWCL list of hazardous chemicals and more common substances that may be 
considered hazardous; establish criteria for identifying, packaging and labeling hazardous 
substances; prescribe management of hazardous substances; establish permit requirements for 
hazardous substances treatment, storage, disposal and transportation; and identify hazardous 
substances that cannot be deposited in landfills. 
Under both RCRA and the HWCL, the generator of a hazardous substance must complete a 
manifest that accompanies the waste from the point of generation to the ultimate treatment, 
storage, or disposal location. The manifest describes the waste, its intended destination, and other 
regulatory information about the waste. Copies must be filed with the DTSC. Generators must 
also match copies of waste manifests with receipts from the treatment, storage, or disposal 
facility to which it sends waste. 
Hazardous Substances Worker Safety Requirements 
Cal/OSHA assumes primary responsibility for developing and enforcing workplace safety 
regulations within the State. Cal/OSHA standards are more stringent than federal regulations. 
Cal/OSHA regulations concerning the use of hazardous substances include requirements for 

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safety training, availability of safety equipment, hazardous substances exposure warnings, and 
emergency action and fire prevention. 
Cal/OSHA enforces the hazard communication program regulations, which include provisions 
for identifying and labeling hazardous substances, describing the hazards of chemicals, and 
documenting employee-training programs. 
Both federal and state laws include special provisions for hazard communication to employees 
who work with and/or encounter hazardous materials and wastes. The training must include safe 
methods for handling hazardous substances, an explanation of MSDS, use of emergency 
response equipment, implementation of an emergency response plan, and use of personal 
protective equipment. 
Groundwater Regulatory Background 
Acting through the RWQCB, the SWRCB regulates surface and groundwater quality pursuant to 
the Porter-Cologne Water Quality Act, the federal Clean Water Act, and Underground Tank 
Regulations. Under these laws, RWQCB is authorized to supervise the cleanup of hazardous 
wastes sites when two conditions are met: (1) the potential for water pollution exists and (2) 
RWQCB assistance is requested by local agencies. 
Depending on the nature of contamination, the lead agency responsible for the regulation of 
hazardous materials at the site can be the DTSC, RWQCB, or both. DTSC evaluates 
contaminated sites to ascertain risks to human health and the environment. Sites can be ranked 
by DTSC or referred for evaluation by the RWQCB. Cal/EPA (DTSC) and Cal/OSHA are 
responsible for ensuring that appropriate measures are taken to protect workers from exposure to 
potential groundwater contaminants. 
Hazardous Materials Transport 
California law requires that Hazardous Waste (as defined above) be transported by a California 
registered hazardous waste transporter that meets specific registration requirements. The 
requirements include: possession of a valid Hazardous Waste Transporter Registration, proof of 
public liability insurance, which includes coverage for environmental restoration, and 
compliance with California Vehicle Code registration regulations required for vehicle and driver 
licensing. 
State agencies with primary responsibility for enforcing federal and state regulations and 
responding to hazardous materials transportation emergencies are the California Highway Patrol 
and the California Department of Transportation (Caltrans). Together, these agencies determine 
container types used and license hazardous waste haulers for hazardous waste transportation on 
public roads. 
Local Regulations 
The Unified Hazardous Waste and Hazardous Management Regulatory Program (SB 1082, 
1993) is a state and local effort to consolidate, coordinate, and make consistent existing programs 
regulating hazardous waste and hazardous materials management. Cal/EPA adopted 

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implementing regulations for the Unified Program (CCR, Title 27, Division 1, Subdivision 4, 
Chapter 1) in January 1996. The Unified Program is implemented at the local level by Certified 
Unified Program Agencies (CUPAs). 
The SJCEHD is the Certified Unified Program Agency (CUPA) for cities and unincorporated 
areas within San Joaquin County (County). SJCEHD regulates the use, storage and disposal of 
hazardous materials by issuing permits, inspecting facilities, and investigating complaints. 
SJCEHD issues permits for installation and removal of aboveground and underground storage 
tanks. SJCEHD inspects businesses for compliance with the Hazardous Waste Control Act which 
places limitations on hazardous waste: storage duration, disposal, and labeling. SJCEHD also 
requires businesses that handle hazardous materials and hazardous wastes to submit an annual 
inventory of hazardous materials and hazardous wastes as well as an emergency response to 
incidents involving those hazardous materials and wastes. 
Emergency Response Plan 
The San Joaquin County Office of Emergency Services has implemented an Emergency 
Response Plan, which is a Hazardous Materials Area Plan. The Emergency Response Plan is 
updated triennially and was most recently updated in 2008. This Plan discusses topics such as 
natural hazards, emergency management, mitigation programs, emergency preparedness, and 
state roles and responsibilities. Under the Plan, considerations have been made for the Port area, 
including the consideration of hazardous materials. 
City of Stockton 2035 General Plan 
The City of Stockton 2035 General Plan contains goals and policies for hazardous materials, 
including the following specific goals and policies that are applicable to the proposed Endicott 
project: 
HS-5 (Hazardous Materials general goal): To minimize the risk to City of Stockton (City) 
residents and property associated with the transport, distribution, use, and storage of hazardous 
materials. 
HS-5.2 Hazardous Materials: The City shall require that hazardous materials are used, stored, 
transported, and disposed of within the City in a safe manner and in compliance with local, State, 
and Federal safety standards. 
HS-5.5 Hazardous Materials Inventory: The City shall require, as appropriate and as a 
component of the environmental review process, a hazardous materials inventory for project 
sites, including an assessment of materials and operations for any development applications. 
Particular attention should be paid to land that previously contained agricultural uses. 
Stockton Municipal Code (Title 15 Buildings and Construction, Chapter 15.12 Fire Code, 
15.12.010 through 15.12.110) 
These portions of the Stockton Municipal Code regulate the construction of buildings and other 
structures used to store flammable hazardous materials, and the storage of these same materials. 
These sections ensure that the business is equipped properly and operates in a safe manner and in 
accordance with all applicable laws and regulations. Permits are issued by the Stockton Fire 

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Department (SFD). The Code also requires maintaining emergency response plans including 
evacuation plans, approved by the SFD. 
6.8.1.3. Required Permits and Approvals 
The U.S. EPA will require Endicott to prepare and submit an SPCC Plan and a Risk 
Management Plan. 
6.8.2. Methodology 
Surrounding potential hazards, hazardous materials, and public health impacts associated with 
the proposed Endicott Project were evaluated through the review of historical records and 
government agency-maintained databases and records of known hazards at the Port, hazardous 
materials contamination, generation, and/or storage as part of the Environmental Database 
Report. Environmental Site Assessments (ASTM 1527-E Phase I Site Assessments) were 
performed on the property in 2013, neither of which revealed existing hazardous conditions on 
the property. 
Four steps have been undertaken to assess the safety impacts and the hazards associated with the 
proposed Endicott project: (1) develop a range of potential upset scenarios associated with the 
proposed Endicott project; (2) estimate the likelihood of the upset scenarios occurring; (3) 
estimate the consequences of the scenarios, should they occur; and (4) determine the significance 
of risk based on the probability of occurrence and the severity of consequences. 
The risk-of-upset analysis evaluates outcomes of potential upset scenarios, which are the 
culmination of several events that result in a hazard to the public and/or environment. Some 
upset scenarios could lead to a significant impact to public safety (e.g., an overpressure in a 
storage tank results in tank rupture, an oil leak, and subsequent fire that reaches a residence and 
results in an injury). Other upset scenarios do not create a significant impact to safety but create a 
significant impact to the environment (e.g., an overpressure in a storage tank results in tank 
rupture, oil leak, and damage to an endangered species habitat). Parts of a given scenario have 
different likelihoods or probabilities. Probabilities and consequences of various project-related 
upset events and scenarios are assessed in this section. 
6.8.3. Environmental Setting 
6.8.3.1. Phase I Site Assessment 
The Port has several sites which have recorded releases of hazardous materials as reported by 
EDR in the EDR Radius Map, Report with GeoCheck, July 30, 2013. The U.S. EPA has reported 
61 sites with reported releases of oil and hazardous substances. Spills of petroleum products at 
Nustar Terminal and Shell Terminal are still open remediation sites. These records were 
reviewed in conjunction with the Phase I Site Assessment completed by TRC in July 2013. 
The July 2013 Phase I Site Assessment encompassed the entire proposed project site (+/- 4.91 
acresÑreport reviewed +/-5.35 acres). No Recognized Environmental Condition (REC) or other 
contamination was found on the property in 2013. 

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Table 6.8-1 includes the findings from the 2013 Environmental Database Report (EDR), 
including known hazardous sites within the region. 
Table 6.8-1: 2013 Environmental Database Report Findings 
Agency Database Survey Distance 
(miles from 
subject site) 
Number 
of Sites 
Identified 
Federal Records 
Federal NPL sites (including de-listed sites) 1.0 4 
U.S. EPA Comprehensive Environmental Response, 
Compensation, and Liability Information System - No Further 
Remediation Action Planned List (CERCLIS-NFRAP) 
1.25 3 
U.S. EPA Resource Conservation and Recovery Act (RCRA) 
Corrective Action (CORRACTS) List 
1.25 1 
U.S. EPA RCRA Registered Large and Small Generators of 
Hazardous Waste (RCRA-LQG) and (RCRA-SQG) 
0.5 3 
U.S. EPA RCRA Permitted Treatment, Storage, and Disposal 
(TSD) Facilities 
0.75 0 
U.S. EPA Emergency Response Notification System (ERNS) 
List 
0.25 1 
U.S. EPA Chemical Hazardous Materials Incident Report 
System (CHMIRS) and Hazardous Materials Incident Report 
System (HMIRS) 
0.25 0 
U.S. EPA National Priority List (NPL) for Superfund Sites 1.25 0 
U.S. EPA Toxic Chemical Release Inventory System (TRIS) 0.25 0 
State and Tribal Records 
State and Tribal NPL equivalent 0.25 1 
State and Tribal CERCLIS equivalent (EnviroStor) 1.25 1 
State Permitted Solid Waste Landfill, Incinerators or Transfer 
Stations (SWF/LF) 
0.75 1 
State and Tribal Leaky Underground Storage Tank (LUST) 0.75 3 
State and Tribal Registered Storage Tanks 0.5 4 
State and Tribal Voluntary Clean-ups 0.75 2 
Local Lists of Landfill / Solid Waste Disposal Sites 0.75 0 
Local Lists of Hazardous waste / Contaminated Sites 1.25 0 

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6.8.3.2. Hazardous Materials at the Proposed Project Site. 
In evaluating the production of biofuel it is important to identify types of hazardous waste(s) 
which may be generated. Potential wastes depend on the catalysts and feedstocks utilized in the 
production process. Under EndicottÕs patented biofuel production, catalysts would likely 
include: ferric chloride, sodium hydroxide, and hydrogen chloride for water treatment 
applications; and proprietary esterification catalysts. Feedstocks would likely include: algae oil, 
tallow, brown grease, choice white grease, poultry fat, used cooking oil, and yellow grease, as 
well as a wide variety of other plant/vegetable/biomass derived oils. 
In the process of using the proposed catalysts, corrosive hazardous wastes may be generated. 
Although biofuel formulations are less toxic than standard petroleum diesel formulations, the 
storage stability of biofuel is less than the standard ultra-low sulfur diesel (ULSD). Degradation 
of biofuels, catalysts, and feedstocks could be caused by temperature, oxidation, and/or material 
incompatibility. Such hazards could be released in the unlikely event that: 
a. Biofuel is leaked or spilled after oxidation and degradation has occurred and hazardous 
substances have resulted; and 
b. Biofuel product is stored beyond the recommended six-month term, becomes a hazardous 
waste. 
These issues must be addressed in the hazards assessments and hazardous waste inventories to be 
performed by Endicott personnel. Additional potentially hazardous byproducts which would 
likely result from the proposed project include Methanol and Glycerin. 
Methanol 
Methanol by itself is not likely to cause environmental harm at levels normally found in the 
environment. However, the proposed project will generate methanol in its biofuel production 
process at levels above those naturally found in the environment. As such, potential exposure to 
methanol may occur in the following media: (1) ingestion through groundwater sources; (2) 
inhalation of methanol; and (3) direct ingestion of or skin/eye contact of methanol. This section 
discusses how methanol is employed in the proposed projectÕs process; safety hazards with 
methanol; and safety mechanisms to be employed at the proposed Endicott project to limit 
potential methanol exposure to Endicott employees, site visitors, and the general public. 
Methanol Use in Proposed Project 
Methanol will be stored in an onsite AST (Aboveground Storage Tank) with a capacity of 10,000 
bbls and will be piped directly from the AST into the Endicott patented biofuel production 
process. The proposed methanol storage tank would be composed of carbon steel construction 
and would have necessary leak detection, foundations, and secondary containment as discussed 
in Section 3.5. Methanol will be utilized in the esterification process as it will be added to free 
fatty acids to assist in the breakdown of free fatty acids into methyl ester. Endicott will utilize 
steam to evaporate and separate methanol from other constituents (water, methyl ether, etc.). 
Methanol Transportation and Handling Regulations 
Methanol is a Class III flammable product as regulated under the United States Department of 
TransportationÕs shipping regulations provided in 49 CFR 172 and 173 and has a flash point of 
11 degrees Celsius. As a Class III product, methanol transporters must comply with federal and 
state safety regulations which include: safety training for personnel handling and shipping the 

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product, registration with federal transportation authorities for the shipment of large quantities 
(5,000 lb. or more) of methanol, federal and state safety protocols in the shipment of methanol, 
and compliance with OSHA standards found in 29 CFR 1910. 
Potential Methanol Hazards at Proposed Endicott Project 
Potential methanol related hazards which could occur at the proposed Endicott project would 
include: 
1. Improper handling methanol (related to import/export process or maintenance); 
2. Leak in piping, equipment, or tank; 
3. Spills from mishandling or leaks; 
4. Fire and/or explosion (methanol is ignited at 11 degrees Celsius); and 
5. Inhalation or combustion from vapors (including potential of hazardous vapors which 
may occur if methanol vapors react with oxides or carbons). 
Endicott will properly train all personnel on the handling of methanol which will include 
discussion of the Material Safety Data Sheet (MSDS) for methanol, including proper medical 
care for direct methanol contact, OSHA and Cal/OSHA regulations for handling methanol, and 
general training related to site safety related to methanol. Drivers transporting methanol would 
be certified and licensed to transport such products. Additionally, the above noted AST and 
facility design will assist in preventing methanol spills and/or contact by Endicott personnel and 
others visiting the site. 
Glycerin 
Glycerin is a combustible substance (flash point greater than 130 degrees Celsius) and is not 
listed as an EPA CERCLA or SARA hazardous substances. Glycerin is also not regulated on the 
DOT hazardous substance or under CaliforniaÕs Proposition 65. Notwithstanding the lack of 
regulation for glycerin, personnel working with glycerin should avoid direct eye, skin, and 
respiratory contact with glycerin. 
Glycerin Use in Proposed Project 
Glycerin would be stored at the proposed project in two ASTs; one of which would be 1,000 
bbls and the second would be 7,500 bbls, both of which will be constructed of 316 SSL stainless 
steel. All ASTs would be designed with necessary foundations and leak detection (and liners as 
needed) to minimize potential spills. Glycerin is a byproduct of the fat splitting process which 
would occur in Unit 1 (triglycerides would be split into fatty acid chains and glycerol through 
the processing which requires the application of steam to the triglyceride, through a series of 
pumps, vessels, and heat exchangers). The Endicott esterification process allows 
glycerin/glycerol to be refined to a point suitable for resale to be employed in a variety of uses 
(initial purification of glycerin would occur in Unit 3; the sweet water evaporation process 
noted in Section 3.5.1.3 above and would be further refined through a process which includes 
distillation, deodorizing, and bleaching aided by a series of pumps and heat exchangers in Unit 
6 as discussed in section 3.5.1.6). The end product of high purity, commercial grade glycerin 
would be sold on the commercial market by Endicott which would reduce the amount of byproduct 
waste to be produced at this facility as compared to traditional biodiesel production facilities. 
Glycerin Transportation and Handling Regulations 
Personnel handling glycerin would be instructed and trained on OSHA standards found in 29 
CFR 1910 which would require personnel to wear eye protection (gloves are advised, but not 

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required) and would provide preventative and responsive safety training. Additionally, when 
handling large volumes of glycerin which could result in significant exposure, personnel should 
wear appropriate National Institute for Occupational Safety and Health (NIOSH) respirators (29 
CFR 1910.134). Endicott would provide a plant/site safety plan which would address chemical 
exposure, including glycerin exposure. 
Potential Glycerin Hazards at Proposed Project 
There would be no additional glycerin hazards at the proposed project area which have not been 
discussed. 
Additional Hazardous Wastes 
Miscellaneous solid wastes which may be generated by the proposed project would include 
wastes from the esterification process (such as animal fats and filtering media); however, it is not 
anticipated that such wastes would be hazardous. This waste would be hauled and disposed of at 
an appropriate landfill. If determined to be hazardous (Endicott personnel or contractors could 
test for known hazards to make this determination), Endicott would store hazardous materials 
within a confined area and would employ an appropriate hazardous waste hauler to haul the 
hazardous waste to an appropriate landfill. 
6.8.3.3. Hazardous Materials which may occur within the Port of Stockton. 
The Stockton Port District is an area of approximately 2,000 acres of existing industrial uses 
related to shipping and receiving of goods and commodities which include hazardous materials. 
Numerous facilities that handle, store, or transport hazardous material are located within the Port. 
The Port handles both hazardous material containers and regulated non-cargo hazardous 
materials. Regulated, non-cargo hazardous materials in the Port may include maritime-use 
compounds such as chlorinated solvents, petroleum products, compressed gases, paints, cleaners, 
fertilizers, and pesticides. Numerous federal, state, and local agencies regulate the storage, use, 
transport, generation, or handling of these materials. The transfer, handling, storage, and 
transport of hazardous liquid bulk cargoes within the Port is planned for by port, regional and 
community plans, and is also under the review of a number of agencies and regulations, 
including the USCG, SFD, SJCEHD- CUPA, and state and federal departments of transportation 
(49 CFR 2 Part 176). 
6.8.4. Standards of Significance 
An impact regarding hazards or hazardous material would be considered significant if the project 
would: 
¥ Create a significant hazard to the public or the environment through the routine transport, use 
or disposal of hazardous materials. 
¥ Create a significant hazard to the public or the environment through reasonably foreseeable 
upset and accident conditions involving the release of hazardous materials into the 
environment. 

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¥ Emit hazardous emissions or handle hazardous or acutely hazardous materials, substances, or 
waste within one-quarter mile of an existing or proposed school. 
¥ Be located on a site which is included on a list of hazardous materials sites compiled 
pursuant to Government Code Section 65962.5 and, as a result, would it create a significant 
hazard to the public or the environment. 
¥ For a project located within an airport land use plan or, where such a plan has not been 
adopted, within two miles of a public airport or public use airport, would the project result in 
a safety hazard for people residing or working in the project area. 
¥ For a project within the vicinity of a private airstrip, would the project result in a safety 
hazard for people residing or working in the project area. 
¥ Impair implementation of or physically interfere with an adopted emergency response plan or 
emergency evacuation plan. 
¥ Expose people or structures to a significant risk of loss, injury or death involving wild land 
fires, including where wild lands are adjacent to urbanized areas or where residences are 
intermixed with wild lands. 
6.8.5. Impacts and Mitigation Measures 
There would be no impacts related to airports, airstrips, fire dangers related to wild lands or 
residential housing, or emergency plans. With construction of the proposed Endicott project, 
these impacts (or lack thereof) would remain the same as no airport/air strip would be located 
within the 2 mile radius, and no wild lands or residences would be constructed in the nearby 
vicinity. 
The following analysis reviews the risk of upset and hazards associated with the proposed 
Endicott project. 
6.8.5.1. Risk of Upset Due to Product Pipeline from Berth #9 to Storage Tanks 
Pipeline Ruptures 
The fatty acid and FAME/B100 pipeline will be operated and maintained by Targa Terminals, 
LLC, which Endicott Biofuel has an agreement for Targa to provide transfer and storage 
facilities to support the Endicott biofuel production facility. Potential impacts to the environment 
from a pipeline rupture has been addressed in the Targa Stockton Terminal Project Tiered Initial 
Study and Mitigated Negative Declaration, State Clearinghouse Number 2012022071, and such 
documentation is incorporated in this Initial Study in its entirety. The Targa pipelines have the 
potential to involve a rupture (spill greater than 100 bbl) based on the Targa pipelines size and 
operating flow rates. Ruptures have significantly lower frequency rates and higher volumes of 
spills than leaks. Likely causes of ruptures involve earthquakes, corrosion, and third-party 
damage. A full rupture scenario assumes a total rupture of a pipeline, resulting in drainage of the 
pipeline content between the two closest valves. 

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In the event of a pipeline rupture, TargaÕs leak detection system (Supervisory Control and Data 
Acquisition System [SCADA]) would be capable of detecting a rupture within two minutes for 
the offloading system and 5 minutes of occurrence for the delivery system, isolating the ruptured 
segment by closing motor operated valves, and shutting down the pumps. These detection times 
are consistent with estimated SCADA leak detection time based on studies presented by the 
National Transportation Safety Board (NTSB) (2005) and Zhang et al (2000) that showed leak 
detection times ranging from 2 to 5 minutes for all leaks larger than 2 percent of the pipeline 
flow rate. Once the pipeline is shutdown, the product would continue to spill until it was drained 
from the affected line. 
The frequency of a release (leak or rupture) is primarily a function of the construction of the 
pipeline, the maintenance and operational practices, as well as third party damage. The volume 
of the subsequent release is a function of the training of the operators as well as the design, 
construction, and maintenance of the leak detection system. The operatorsÕ actions are accounted 
for in the pipeline failure frequency analysis by assigning a high probability of operator error, 
particularly related to the operation of the SCADA system. As such, the proper utilization of the 
SCADA system would limit several foreseeable impacts, and therefore, would leave impacts due 
to pipeline ruptures less than significant. 
Pipeline Leaks 
Pipeline leaks (spills less than 100 bbl) are similar to ruptures described above, except that they 
address smaller-sized releases from the pipeline. This distinction has been made between leaks 
and ruptures to account for the different failure frequencies that exist between ruptures and leaks. 
Pipeline leaks are most commonly a result of corrosion, erosion, or third party damage to the 
pipeline. TargaÕs pipeline leak detection system would use a volume based monitoring system, as 
well as pressure monitoring. Because pressure would not change significantly due to a smaller 
leak, small leaks are difficult to detect using a SCADA system and volume monitoring is 
generally used to assist in the detection of small leaks. Typically, a small corrosion-induced leak 
would have a leak rate of 1 to 2 barrels per hour. In the event that a potential leak is detected, the 
pipeline would be shut down until it could be fully inspected. Typically, pipeline leaks have 
much smaller spill volumes than pipeline ruptures (CSFM 1993), thus evading rapid detection. 
Pipeline Leak Detection System 
A leak detection system would be installed for all pipeline systems associated with the proposed 
Endicott project. The system would automatically alert the operator if a leak occurs so that 
appropriate actions can be taken to minimize the spill volume and duration. The system would be 
designed to protect the public and the environment from the consequences of a pipeline failure 
and uncontrolled spill by greatly minimizing the frequency of a pipeline failure and spill. 
The overall Leak Detection Systems would be designed in accordance with API Standard 1130, 
ÒComputational Pipeline MonitoringÓ, with performance in accordance with API Standard 1149, 
ÒPipeline Variable Uncertainties and Their Effects on Leak DetectabilityÓ. Specifically, the 
project would utilize a Real Time Transient Model (RTTM) system to monitor the pipelines, as 
defined in API 1130. This method employs numerous monitored variables and a sophisticated 
computer model to identify upsets or potential leaks. The reason for monitoring different 
variables is to increase the likelihood of prompt leak detection. The input to the computer would 

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include operating parameters for temperature, pressure, flow, viscosity and density, and include 
equipment input such as pump start/stop and valve open/close signals. The output from all of the 
sensors would be compared against a baseline model. Values that differ from the modeled case 
would indicate a potential leak. The control center operators, who are responsible for monitoring 
the system at all times, would respond to all potential leak conditions by verifying the condition 
and taking appropriate action as identified in Endicott pipeline operations manual or following 
pipeline safety guidelines, which would be kept at the facility. 
In addition to the RTTM system, two additional monitoring and analysis methodologies would 
be employed to verify pipeline integrity: Volumetric Balancing (modeling for fluctuations in line 
pack, as well as the basic volumetric balance calculations) and Pressure/Flow Monitoring 
(monitors for rapid changes in the pressure and/or flow rate). 
As noted earlier, the proposed pipeline system would be monitored and controlled by Targa 
operators. Targa anticipates using commercially available pipeline software to perform the leak 
detection functions. The system would reside in the Control Building on a dedicated processor 
(with dedicated screen) and collect data from the SCADA system. The data polling cycle 
(request and time combined) to all field locations is estimated to be 1-5 seconds or less. 
The expected performance of the leak detection system, as defined by the API standards 
referenced above, as the leak detection time vs. the leak flow rate as a percent of the design 
pipeline flow rate. The proposed system would be able to detect a potential leak as small as 0.71 
percent of the design flow in 5 minutes or less. At the design flow rate for the vessel unloading 
pipeline system (Berth #9 to Storage Tanks) of 10,000 barrels per hour, this relates to a flow rate 
of 1.8 barrels per minute. Leaks of less than 100 barrels per hour would be detected through line 
balancing, with an approximate detection time of 10 to 12 hours. 
When the pipeline system is in a shutdown condition, the leak detection system would continue 
to monitor for leaks by tracking the pressure and temperature of the system. Any unexpected 
changes would trigger alarms and alert the pipeline operators of the potential problem. The 
systemsÕ ability to detect a leak during this period would increase dramatically as a result of the 
flow rate variable being removed from the system modeling. 
If a leak is detected, the system would be designed to quickly isolate the leak and minimize the 
amount of a release. In addition to continuous monitoring, the SCADA system will provide the 
pipeline controllers with the ability to remotely control important aspects of systems operation, 
including starting and stopping pumps, opening and closing valves, switching into and out of 
storage tanks and facility emergency shutdowns. The SCADA system will be programmed to 
alert the pipeline system controllers any time that operational conditions fall outside established 
parameters. Upon detection of an irregularity, the pipeline system controllers will have the 
capability to shut down the affected terminal equipment or pipeline by remotely stopping pumps 
and closing block valves that will be part of the various systems. Additionally, Emergency 
Shutdown (ESD) buttons will be installed at key locations around the facilities, allowing system 
operators to safely halt operations in case of an emergency. 

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To assure optimal operations at all times, the proposed SCADA system would have multiple 
levels of redundancy to provide robust real-time operation, including redundant backup servers 
for critical applications. The system proposed would use a high-speed fiber optic 
communications systems and T1 communications circuits to transmit and collect data as rapidly 
as possible. The proposed communication infrastructure would support polling of remote devices 
such as pumps, meters, valves, tanks, pressure and temperature instruments numerous times each 
minute. 
Electronic leak detection and continuous, reliable monitoring systems are only two components 
of an overall pipeline mechanical integrity program. Other components include: proper 
construction methods; pipeline coatings; cathodic protection systems; pipeline patrols; internal 
pipeline inspections (smart pigs); and external inspection of above grade pipe. Since these lines 
are relatively short and located in high traffic areas, any potential issues will be quickly detected. 
Warning signs would be posted along the ROW, alerting people as to the presence of the lines. A 
contact phone number will also be provided. 
6.8.5.2. Fire Hazards 
Generally, biofuels are safe substances which present low fire risk. However, biofuel 
processing, itself, may present potential risk for fire hazards. Such hazards generally result due 
to the methanol stored on site from a given operation. Methanol is a highly flammable substance 
which burns with an invisible flame, making it difficult to protect against. Recently, a survey of 
biofuel plant operations after fires had occurred demonstrated that almost all accidents refer to 
methanol vapors. In some cases, domino effects resulted in larger fire outbreaks (methanol fire 
caught biofuel and feedstock stored in the plant on fire). 
To protect against fire hazards, Endicott biofuel production facility personnel will go through 
chemical spill and fire response training in order to help preserve property, and personnel safety. 
Such training will include general information, such as informative training on MSDS for 
chemicals present at the site, fire and safety training (including storage locations, designated 
work locations, designated smoking/non-smoking areas, etc.), and other training in accordance to 
Occupational Safety and Health Administration (and CalOSHA), International Fire Code 
standards, and supporting local or state safety protocols. In addition, state of the art Fire 
suppression systems will be designed and dedicated to the Endicott biofuel production facility. 
Fire protective equipment (fire extinguishers, signage, and fire protective clothing) will be 
available in several locations throughout the biofuel production facility. Fire emergency exits 
will be clearly labeled for ease of access. Endicott personnel will be trained on the operations of 
the fire safety systems. With the above describe training program, fire suppression systems at 
the biofuel production facility, risks of fire hazards will be managed within acceptable risk 
factors and the proposed Endicott project will not have a significant impact on fire hazards. 
6.8.5.3. Public Safety 
Sensitive public receptors are those locations such as residences, schools, daycare centers, etc. 
which might have persons present for extended periods of time, and thus would be potentially 
affected by a nearby catastrophic event. In the event of an accident in the vicinity of a sensitive 
receptor, consequences of the accident could be much greater than at other locations. There are 

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no sensitive receptors located near the proposed Endicott biofuel production facility. The nearest 
sensitive receptor is the George Washington Elementary School which is located 1.3 miles east 
of the proposed project area. 
Potential impacts to the public are determined by delineating Òhazard footprintsÓ for the type of 
accidents that can potentially occur. It is then determined if the hazard footprints would reach the 
sensitive receptors or vulnerable resources identified in the area, as well as the number of injuries 
and/or fatalities that could occur. Types of hazards evaluated include radiant heat from a fire, 
flammable gas cloud from a release, and blast overpressure and flying debris from an explosion. 
Due to the large distance from any component of the proposed Endicott project and the closet 
sensitive receptor, no significant impact is anticipated from the risk of upset. The following 
mitigation measures have been incorporated to diminish any potentially significant impacts 
related to hazards and hazardous materials to a less than significant level: 
HM-1 Provide all employees and the Stockton Port District with a hazardous materials 
business plan that educates employees on handling and shipping of hazardous 
materials. 
HM-2 Design facilities with secondary containment for all ASTs. 
HM-3 Design all ASTs with under-tank leak detection that would meet the requirements 
of API 650. 
HM-4 Each tank foundation would have a membrane liner, which would be constructed 
of High Density Polyethylene, thereby ensuring any potential leakage is contained 
to the maximum extent possible, within the foundation area of the tank. 
HM-5: Endicott to document MSDS are made available to each employee assigned to 
work with methanol, nitrogen, glycerin, pitch, or biofuels. The MSDS should 
include specific information on the material, and should list all pertinent 
information including flashpoint, boiling point, acute and chronic effects of all 
chemical ingredients in the solution, protective equipment, as well as other fire 
and emergency cleanup information. 
HM-6: Provide the Port Fire Department with a plant/site safety plan which shall be 
updated as needed. 
HM-7: Employ leak detection (SCADA) for all pipelines to ensure that leaks are 
discovered, and all flow is shut-off, as quickly as possible. 

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6.8.6. Hazards and Hazardous Materials Initial Study Responses 
Table 6.8-2: Hazardous Waste Initial Study Responses 
WOULD THE PROJECT: 
Potentially 
Significant 
Impact 
Less Than 
Significant 
Impact with 
Mitigation 
Incorporated 
Less Than 
Significant 
Impact 
No 
Impact 
a) Create a significant hazard to the public or 
the environment through the routine 
transport, use, or disposal of hazardous 
materials? 
. . . . 
b) Create a significant hazard to the public or 
the environment through reasonably 
foreseeable upset and accident conditions 
involving the release of hazardous materials 
into the environment? 
. . . . 
c) Emit hazardous emissions or handle 
hazardous or acutely hazardous materials, 
substance, or waste within one-quarter mile 
of an existing or proposed school? 
. . . . 
d) Be located on a site which is included on a 
list of hazardous materials sites compiled 
pursuant to Government Code 65962.5 and, 
as a result, would it create a significant 
hazard to the public or the environment? 
. . . . 
e) For a project located within an airport land 
use plan or, where such a plan has not been 
adopted, within two miles of a public airport 
or public use airport, would the project result 
in a safety hazard for people residing on 
working in the project area? 
. . . . 
f) For a project within the vicinity of a private 
airstrip, would the project result in a safety 
hazard for people residing or working in the 
project area? 
. . . . 
g) Impair implementation of or physically 
interfere with an adopted emergency 
response plan or emergency evacuation 
plan? 
. . . . 
h) Expose people or structures to a significant 
risk of loss, injury, or death involving 
wildland fires, including where wild lands are 
adjacent to urbanized areas or where 
residences are intermixed with wild lands? 
. . . . 

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6.8.7. Responses to Initial Study Questions 
6.8.7.1. Significant Hazard to the Public or Environment through Transport or Use of 
Hazardous Materials: Less than Significant with Mitigation 
The project design minimizes the risk of hazardous materials release through appropriate 
technological development and design; some of these design factors are required by law, as 
previously discussed, and others will be implemented as mitigation measures, and will receive 
additional treatment in subsequent portions of this document. In addition to the construction of 
impervious surfaces for vehicle transportation and maintenance, secondary containment of each 
above ground storage tank would contain one hundred percent of the largest tank plus additional 
freeboard for rainfall as required by 40 CFR 112.8. Curbing would also be constructed 
surrounding the ISBL to contain any fluid which may be released in the biofuel production 
process. Additionally, Endicott would prepare, submit, and implement a hazardous materials 
business plan which would ensure all employees, including drivers, handlers, and haulers are 
adequately trained on handling the hazardous materials, as directed in the above listed mitigation 
measures. Furthermore, Endicott would submit this document to the Stockton Port District prior 
to construction (to ensure the Office of Emergency Services is well informed with any potential 
hazardous materials on the proposed Endicott site and to allow the Port to provide any additional 
training it deems necessary). Likewise, Endicott would be required to develop and implement a 
hazardous materials plan would be inspected by the Stockton Office of Emergency Services to 
ensure proper implementation and related training. Therefore, this impact would be less than 
significant with the implementation of the discussed mitigation measures and design factors. 
6.8.7.2. Significant Hazard to the Public or Environment through Reasonably 
Foreseeable Accident: Less than Significant with Mitigation 
As previously discussed, the typical foreseeable accident would include the leak or rupture of a 
pipe or tank that may occur with varying discharge rates. To limit the potential of any such 
discharge, Endicott would train personnel on properly handling hazardous materials. Such 
training would be accomplished in conjunction with the development and implementation of a 
hazardous materials business plan which is required by law. Additionally, Endicott proposes 
utilizing a design which limits the potential of spills or leaks that reach offsite locations. Such 
design features include the following, each of which was listed as a mitigation measure in 
Section 6.8.5: 
¥ Under-tank leak detection would be provided for each of the fuel storage tanks. The leak 
detection system would meet the requirements of API 650. Such a leak detection system 
would alert Endicott staff should any leaks occur, thereby ensuring quick action in the event 
of a spill. Such a timely response would ensure that any such spill is controlled as close to the 
onset as possible. 
¥ Each tank foundation would have a membrane liner, which would be constructed of High 
Density Polyethylene, thereby ensuring any potential leakage is contained to the maximum 
extent possible, within the foundation area of the tank. 

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¥ The site has been designed with a buffer/berm area between the site and additional facilities 
and the San Joaquin River. This berm would limit the potential of off-site environmental 
contamination. 
¥ Training to Endicott employees would be completed with the preparation, submission, and 
implementation of a hazardous materials business plan. 
6.8.7.3. Emit Hazards within 0.25 Mile of a Proposed or Existing School: Less than 
Significant with Mitigation 
The nearest existing school is the George Washington Elementary school 1.3 miles from the 
proposed Endicott biofuel production facility. No school has been proposed within the 0.25 mile 
radius of the proposed facilities. As the entire Port area is zoned PT, it is unlikely that a school 
would be constructed within this radius. The proposed Endicott project will have no impact. 
6.8.7.4. Located On a Hazardous Materials Site: No Impact 
As determined by the EDR, the proposed Endicott project is not located on a hazardous materials 
site (See Appendix F for Phase I ESA). No impact. 
6.8.7.5. Create a Safety Hazard for People Working or Residing Within 2 Miles of a 
Public Airport: No Impact 
The Stockton Metropolitan Airport is the nearest airport to the proposed project area and is 
roughly 6 miles to the southeast. As such, the proposed project area does not pose a threat to the 
safety of those residing or working within airport zones. The site is surrounded by industrial 
uses, a police training facility, and a wastewater treatment facility and no airports or airstrips. As 
such, there will be no impact to a nearby airport. 
6.8.7.6. Create a Safety Hazard for People Working or Residing Within the Vicinity of a 
Private Airstrip: No Impact 
No private airstrip is within the vicinity of the proposed project area and as such, the proposed 
project area does not pose a threat to the safety of those residing or working within airstrip area. 
No impact to airstrips would occur from the proposed Endicott project. 
6.8.7.7. Physically Impair or Interfere with the Implementation of an Emergency 
Response Plan: No Impact 
The locally implemented Emergency Response Plan is a Hazardous Materials Area Plan that has 
been developed and implemented by the San Joaquin County Office of Emergency Services. 
(Stockton is one of several facilities that have an agreement with the County Office to operate 
within the parameters of the Plan). The Emergency Response Plan is updated triennially and was 
most recently updated in 2008. Under the Plan, considerations have been made for the Port area, 
including the consideration of hazardous materials. Therefore, the construction of the proposed 
Endicott project would not result in an impact on the implementation of the CountyÕs Emergency 
Response Plan. 

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6.8.7.8. Create Risk Involving Wildfires or Wildlands: No Impact 
No wildland is within the vicinity of the Port, and as such, the proposed Endicott project does not 
pose a threat to destruction of any such lands. The site is surrounded by industrial uses, a police 
training facility, and a wastewater treatment facility and no wild lands. Therefore, there would be 
No Impact to wildfires or wild lands. 

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6.9 Hydrology and Water Quality 
This section analyzes the potential impacts on water quality and hydrology that may result from 
the proposed Endicott project located in the San Joaquin River Hydrologic Region. Additionally, 
this section addresses the following potential issues related to the implementation of the 
proposed Endicott project: general water quality issues, flood hazards, storm drainage issues, and 
project-specific impacts on the City of StocktonÕs (City) Regional Wastewater Control Facility. 
These data sources were supplemented by observations made during site visits conducted during 
the months of July and August 2013. 
6.9.1. Background 
6.9.1.1. Regulatory Context 
The water surface quality is federally regulated by the Environmental Protection Agency (EPA). 
In California, the SWRCB and its RWQCBs regulate groundwater quality. The RWQCB is the 
primary agency tasked with protecting California surface and groundwater quality, including the 
regulation of discharges from wastewater treatment facilities and of urban stormwater runoff. 
The RWQCB for the Central Valley Region has established a Water Quality Control Plan 
(WQCP) for the Sacramento and San Joaquin River Basins that designates surface and ground 
waters in the region and assigns beneficial uses to such waters. Additionally, the WQCP and 
establishes water quality objectives to protect those waters. The water quality objectives and 
beneficial uses are collectively referred to as Water Quality Standards. 
Federal Regulations 
The Clean Water Act (CWA) (33 USC 1251-1376), is the federal legislation that governs water 
quality. The objective of the CWA is Òto restore and maintain the chemical, physical, and 
biological integrity of the NationÕs waters.Ó 
Applicable sections of the act are as follows: 
¥ Section 301 prohibits the discharge of any pollutant by any person, except as in compliance 
with sections 302, 306, 307, 318, 402, and 404 of the CWA. 
¥ Sections 303 and 304 provide for water quality standards, criteria, and guidelines. 
Section 303(d) of the CWA requires states to develop a list of impaired water bodies. In 
California the SWRCB has developed the list of impaired waters, applying the following criteria: 
chlopyrifos, DDT, dianzion, Group A pesticides, mercury, unknown toxicity, and organic 
enrichment/low Dissolved Oxygen (DO). Due to low DO levels, the San Joaquin River Deep 
Water Shipping Channel (SJDWSC) has been placed on the impaired list. (SWRCB Total 
Maximum Daily Load [TMDL] Ñ SWRCB, 2011). Due to these impairments, the proposed 
Endicott project would necessarily need to operate within the parameters of the TMDL and all 
other water quality standards as discussed below. 

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State Regulations 
Porter-Cologne Water Quality Control Act 
The Porter-Cologne Water Quality Control Act (California Water Code ¤ 13000 et seq.), which 
is the principal law governing water quality regulation in California, establishes a comprehensive 
program to protect water quality and the beneficial uses of State waters. The Act established the 
SWRCB and nine RWQCBs, which are charged with implementing its provisions and which 
have primary responsibility for protecting water quality in California. The Porter-Cologne Water 
Quality Control Act also implements many provisions of the federal CWA, such as the NPDES 
permitting program. CWA ¤ 401 gives the SWRCB the authority to review any proposed 
federally permitted or federally licensed activity which may impact water quality and to certify, 
condition, or deny the activity if it does not comply with State water quality standards. If the 
SWRCB imposes a condition on its certification, those 20 conditions must be included in the 
federal permit or license. 
RWQCB Construction Permit 
The RWQCB administers the NPDES stormwater permitting (federal stormwater permitting 
program which is implemented by each state) program in the Central Valley Region for 
construction and industrial activities. Because the proposed site is an industrial site which would 
require construction prior to its operation, Endicott Biofuels (Endicott), would be required to 
obtain both a construction and industrial NPDES permit from the RWQCB prior to construction 
and/or operation. 
To require a construction permit, a construction site must disturb one acre or more of land (this is 
more commonly referred to as a General Construction Permit). Qualifying projects require the 
applicant to submit a Notice of Intent (NOI) to the SWRCB prior to the beginning of 
construction. The General Construction Permit requires the preparation and implementation of a 
Stormwater Pollution Prevention Plan (SWPPP), which must be completed before construction 
begins. The SWPPP must describe the BMPs and monitoring programs that would be 
implemented during the construction phase to ensure that runoff from the construction site does 
not cause or contribute to exceedances of water quality standards relevant to receiving waters 
downstream of the site. Implementation of the plan starts with the commencement of 
construction and continues through the completion of the project. Upon completion of the 
project, the applicant must submit a Notice of Termination to the RWQCB to indicate that 
construction is completed. 
RWQCB General Industrial Permit 
For industrial sites, such as the proposed project area, a General Permit for Discharges of 
Stormwater Associated with Industrial Activities (General Industrial Permit--GIP) is required. 
Under the industrial site, operators must submit an NOI to the SWRCB prior to commencing 
operations. The GIP also requires that a SWPPP discussing stormwater and dry weather runoff 
BMPs and monitoring programs be prepared prior to the commencement of operations. The 
BMPs must meet the technical design standards required by the GIP and must ensure that runoff 
from the site does not cause or contribute to exceedances of Water Quality Standards relevant to 
the siteÕs receiving waters. The SWPPP must be implemented as long as industrial activities are 
ongoing. 

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As the Port is recognized by the State as an independent municipality, the Port possesses the 
permitting status of any other municipality. As a result, the Port has been issued a Municipal 
NPDES Permit by the RWQCB. This permit prohibits discharges from the PortÕs storm drain 
system from exceeding water quality standards in the local receiving waters. The Port has 
implemented a comprehensive SWPPP under this permit to minimize impacts to water quality 
from the urban runoff flowing through its storm drain system. The Port administers a Port-wide 
Municipal Stormwater Management Program, which includes participation by Port tenants. The 
PortÕs municipal NPDES permit does not relieve tenants of their individual responsibility for 
compliance with industrial and construction stormwater permit regulations, or requirements to 
obtain individual NPDES permits for point-source discharges. Runoff from the proposed 
Endicott project would enter the PortÕs storm drain system, and would, therefore, be subject to 
the PortÕs SWPPP and Stormwater Management Program implemented pursuant to the PortÕs 
municipal NPDES permit. 
California Toxics Rule (CTR) of 2000 (40 CFR Part 131) 
This rule establishes numeric criteria for priority toxic pollutants in inland waters as well as 
enclosed bays and estuaries to protect ambient aquatic life (23 priority toxics) and human health 
(57 priority toxics). The CTR also includes provisions for compliance schedules to be issued for 
new or revised NPDES permit limits when certain conditions are met. The numeric criteria are 
the same as those recommended by the EPA in its CWA Section 304(a) guidance. 
Spill Prevention, Control, and Countermeasure 
SPCC regulations require the Port to have in-place measures that help ensure spills do not occur. 
However, if they do, there are protocols and response equipment in place to contain the spill and 
neutralize the potential harmful impacts. A SPCC Plan would be prepared that would be 
reviewed and approved by the Regional Water Quality Control Board. The SPCC Plan would 
detail and implement spill prevention and control measures. 
Local Regulations 
The City of Stockton operates the receiving wastewater treatment facility for waters from the 
proposed Endicott project. The CityÕs treatment plant is subject to its own NPDES permit. The 
City, to ensure compliance with its NPDES permit, requires industrial operations to obtain an 
Industrial Waste Discharge Permit for the discharge of domestic wastewater and project processrelated 
wastewater to its treatment facility. These permitting requirements are found in the 
CityÕs Ordinance 13.08: Wastewater Discharges and Treatment Works. Ordinance 13.08 
requires all dischargers to obtain a discharge permit from the City prior to the commencement of 
operations. This discharge permit will contain specific numeric criteria for the flows entering the 
treatment plant from the proposed Endicott project and would require Endicott to monitor its 
flows (ensuring adherence to these numeric criteria). 
In addition to adherence to the CityÕs NDPES permit, Endicott would be required to comply with 
the PortÕs Stormwater Development Standards Plan, under its municipal NPDES permit 
programs. Pursuant to the PortÕs Plan, Endicott would be required to implement certain BMPs 
designed to control sources of pollutants including: 

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¥ Storm drain signage (e.g., signs stating Òno polluting flows to riverÓ); 
¥ Specific requirements related to the design of certain outdoor areas used for material storage, 
trash storage, loading docks, vehicle/equipment maintenance, vehicle/equipment washing, 
and fueling (to prevent or reduce the potential for stormwater runoff to contact potential 
pollutants in these areas); 
¥ Tracking controls for transitions between paved and unpaved areas (to reduce the potential 
for sediment tracking onto paved roadways); and 
¥ Specific design requirements for open drainage culverts (to prevent erosion and reduce storm 
flow velocities). 
Additionally the Stormwater Development Standards require that the project applicant treat 
runoff from the area of new development (from the newly created impervious area). The selected 
treatment device may consist of one or more BMPs, such as: vegetated swales, extended 
detention basins, and media filters (that meet specified design requirements to treat small rain 
events and the initial portion of larger rain events). Specifically, the treatment devices must 
capture and treat a volume of rain to be produced from a 24-hour 85th percentile storm event (the 
maximum flow rate of runoff produced by the 85th 
percentile hourly rainfall intensity multiplied 
by a factor of two). 
6.9.2. Methodology 
This analysis considers the potential for the proposed Endicott project impacts to local surface 
and groundwater hydrology and water quality. The impact analysis focuses on foreseeable 
changes to existing hydrological and water conditions. The impact analysis provides a separate 
discussion for major proposed Endicott project components. Potential water and sediment quality 
impacts of the proposed Endicott project are assessed through a comparison of literature data 
(including all applicable water quality criteria) and results from past projects in the Port, to 
estimated discharges from the proposed Endicott project using scientific expertise of the 
preparers. Mitigation measures are identified where appropriate. 
6.9.3. Environmental Setting 
6.9.3.1. Project Setting 
Water Supply 
The proposed project will require water supply for several facets of the proposed project, 
including: domestic water supply for the necessary personnel facilities, water supply for the 
production facilities, and temporary water supply for construction efforts. The water purveyor 
for the proposed lease area is the California Water Service Company (CWSC). There is a water 
line in Navy Drive adjacent to the proposed project area. This water line is 16Ó in diameter and 
is composed of asbestos cement pipe and will provide service to the control 
room/admin/laboratory building, ISBL, water cooling tower, and emergency showers. The 16Ó 
line will provide 11,520,000 gallons per day (GPD) water flow capacity with an assumed 
velocity in feet per second of 14.5 and Head Loss in feet per 100 feet of 3.5. A ÒWill ServeÓ 

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letter/email describing the CWSCÕs water supply capabilities in included in the TRC Engineering 
Feasibility Report (Appendix H). 
The proposed Endicott project water estimates assumed operational water consumption factors of 
10,000 gallons per day of process water involved in the biofuel production process and office use 
of water with an additional 22,000 gallons per day of cooling water associated with the biofuel 
production process. It is estimated that the proposed Endicott project operational total office and 
biofuel production industrial use water demands will be approximately 493,277 gallons per day, 
with Fire Protection Water Flow Demands of 2,000 gallon per minute. 
Water supply needs are summarized in the TRC Engineering Feasibility Report (Appendix H). 
Construction water requirements have been calculated at roughly gallons for the entire 
construction period. 
Potable Water Demands 
Potable water demand has been calculated at 563 GPD. These calculations were based on 
proposed personnel (20 individuals) required to operate the biofuel production facility, square 
footage of buildings (Utilities Building, office/administrative building, and the Motor Control 
BuildingÑeach of which is no greater than 1,000 square feet) were included in the area 
designated for industrial uses) required for the proposed project, and requirements for emergency 
equipment (emergency showers for drivers and plant personnel). The calculations were based on 
industry standard which indicates that a 1,000 square foot building will require roughly 80 GPD 
for utilization. 
Biofuel Production Water Demands 
Production demands will vary, but the general rule for the site is that the production process will 
require roughly 22,000 GPD or 15 Gallons per Minute (GPM). This water will be provided from 
CWSC; TRC has verified with CWSC that the provision of this amount of water is feasible and 
will not result in over demand to CWSCÕs system. 
The proposed Endicott project will utilize the proposed water consumption to produce biofuels 
and to cool equipment which is broken down into several ÒUnits.Ó In Unit 1, water will break 
fatty acid chains from glycerol, transforming the water into a dilute solution of water and 
glycerin known as Òsweet waterÓ. During this process, high and low steam pressure will be used 
to split the fatty acids. The result will be sweet water (a byproduct of the free fatty acid 
breakdown which is a combination of water and glycerin). In Unit 2, the sweet water will be 
processed to eliminate unnecessary residual free fatty acids with using ferric chloride (FeCl3), 
sodium hydroxide (NaOH), hydrogen chloride (HCl), filter aid, silica, and low steam pressure. 
In Unit 3, the glycerin and the water in the sweet water will be separated via evaporation which 
will require the application of medium pressure steam, and will produce wastewater effluent. 
Effluent will be stored, treated, and pumped away. In Unit 4, the free fatty acids will be 
processed through a vacuum distillation process which will require water for medium and low 
pressure steam. In Unit 5, the esterification process creates the FAME/B100 and requires 
medium and low pressure steam. Effluent will be treated, and stored as a byproduct of this 
process. In Unit 6, glycerin from Unit 3 is refined using medium and low pressure steam and 
will also result in effluent waste water. As noted previously, the water required for the 
production process will be provided from CWSC; TRC has verified that CWSC that the 

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provision of this amount of water is feasible and will not result in a lack of supply in CWSCÕs 
system. 
Construction Water Demands 
The construction phase of the proposed Endicott project is expected to occur over a nine (9) to 
eleven (11) months. During this time period, construction activities would require a total water 
demand of approximately 500,000 gallons. Primary consumption would occur during the 
grading and excavation phase of construction to dampen soil to reduce potential fugitive dust 
emissions and to assist in the dirt compaction process. To mitigate effects of Òtrack outÓ (soil and 
other material brought off site by vehicle tires), it is expected that gravel areas will be sufficient. 
Therefore, water is not expected to be used in washing vehicles. However, if it does become 
necessary to use water to wash tires or any other equipment, the water and any contaminants it 
contains (i.e. total suspended solids, soap, oil) will be contained, pre-treated if possible, and 
pumped directly to the nearby water treatment plant. 
Stormwater Bioretention Basin 
All stormwater within this complex drains to a stormwater detention basin south of the proposed 
Endicott project (the detention pond is immediately adjacent to the proposed Targa Storage 
facility south of EndicottÕs proposed project). Storm water is not discharged from this detention 
basin until a high level is reached. During years when the detention basin reaches a high level, 
stormwater is pumped to the San Joaquin River. 
The proposed project will convey stormwater runoff to an on-site stormwater bio retention basin 
which will hold stormwater until piped off site. The bio retention basin has been sized to 
accommodate runoff from both the Endicott Site as well as Navy Drive (immediately west of the 
proposed project area). The proposed stormwater bio retention basin would be approximately 
150Õ x 28Õ with 2:1 side slopes and would be designed to accommodate stormwater runoff, 
including major weather events, thereby preventing it from flowing directly into the San Joaquin 
River. The collected water would infiltrate to an underground slotted pipe which would catch the 
flow and convey it to the Port of Stockton storm water detention basin through a connection to 
the 42Ó storm drain that runs along Navy Drive. If a high level is reached in the onsite 
stormwater bio retention basin, the collected water would overflow to the 42Ó storm drain and 
would be pre-treated (as needed) and piped off-site. Additional discussion related to stormwater 
discharges will be provided in the Utilities Section of this document (Section 6.17). 
6.9.3.2. Regional Setting 
Port of Stockton 
The proposed Endicott project is within the Port, which is located within the San Joaquin River 
Basin. Average annual precipitation in Stockton is 13.7 inches (General Plan Background 
Report 2004). The proposed project area is flat and nearly featureless with the topography 
sloping southwest towards Navy/Washington Drive. The project area is primarily flat through 
the entire property, with a very slight slope to the southwest toward Navy Drive, and is bordered 
on the north by the San Joaquin River. The project area is not located in an area subject to 
inundation by seiche, tsunami, or mudflow, and it is not adjacent to topographic elevations which 
would induce or permit mudflow. 

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The proposed project area is protected by a levee system. Levee failure has a relatively small 
probability of occurrence (levees may be subject to site specific structural failure, erosion, 
damage from vegetation and rodents, and earthquakes). The Port is responsible for the levee 
system and has established an annual levee monitoring and inspection program. The purpose of 
the program is to determine whether reinforce the structural integrity of the perimeter levee is 
required. 
San Joaquin River and Delta 
The Sacramento - San Joaquin River Delta (Delta) is a 1,150-square-mile, triangular region of 
land and water at the confluence of the Sacramento and San Joaquin Rivers (U.S. EPA, 1996). 
The DeltaÕs waterways comprise a matrix of aquatic habitat of approximately 75 square miles, 
and extend from Suisun Bay, in the west, to the cities of Sacramento and Stockton to the north 
and east. Major inputs of freshwater to the Delta are from the Sacramento River in the north and 
the San Joaquin River in the south, while tidal fluctuations bring salt water from Suisun and San 
Francisco Bays, with which the Delta forms an interconnected estuary system. The proposed 
project area is located on the San Joaquin River, several miles inland of Suisun or San Francisco 
Bay; however, due to tidal conditions and vessel travel through the Delta channels, the Delta has 
increased salinity which results in brackish conditions which are ideal permanent residence and 
as a migratory route for several species including Chinook salmon and steelhead trout (protected 
species). 
6.9.3.3. Flooding 
The County of San Joaquin maintains Flood Insurance Risk Maps (FIRMs) as required by the 
Federal Emergency Management Agency (FEMA). These FIRMs indicate potential of flooding 
for various locations. The proposed project area is located in an ÒX (levee)Ó zone which 
indicates that due to the vicinity of the San Joaquin River levee, the potential of the proposed 
project area being affected by a 100-year flood event is less than 1%. Furthermore, the project 
area is not located in an area subject to inundation by seiche, tsunami, or mudflow, and it is not 
adjacent to topographic elevations which would induce or permit mudflow. 
6.9.3.4. Storm Drainage System 
The Port has developed a Stormwater Development Standards Plan (DSP). The project is south 
of Washington Street and within the DSPÕs East Complex. All stormwater within this complex 
drains to a stormwater detention basin. During years when the detention basin reaches a high 
level, stormwater is pumped to the San Joaquin River (Stockton Port District Stormwater 
Development Standards Plan, 2006). The Stockton Port District DSP specifies a number of 
BMPs. All stormwater within this complex drains to a stormwater detention basin located 
southeast of the Targa storage site. Storm water is not discharged from this detention basin until 
a high level is reached. During years when the detention basin reaches a high level, stormwater 
is pumped to the San Joaquin River (Port of Stockton Stormwater Development Standards Plan, 
Revised April 17, 2006, Page 3).