##### Table of Contents



UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 FORM 10-K
  þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 FOR THE FISCAL YEAR ENDED DECEMBER 31, 2009
 OR
 o
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 FOR THE TRANSITION PERIOD FROM  TO .
 Commission file number: 001-32567
 ALON USA ENERGY, INC.
  Delaware
(State of incorporation)
    
    74-2966572
(I.R.S. Employer Identification No.)7616 LBJ Freeway, Suite 300, Dallas, Texas
(Address of principal executive offices)
    
    75251
(Zip Code)
   Title of each class
    
    Name of each exchange on which registeredCommon Stock, par value
    
    New York Stock Exchange$0.01 per share
  o þ
 o þ
 þ o
 o o
 o
  Large accelerated filer o
Accelerated filer þ
Non-accelerated filer o(Do not check if a smaller reporting company)
Smaller reporting company o o þ




---



##### 



TABLE OF CONTENTS
 PagePART IITEMS 1. AND 2. BUSINESS AND PROPERTIES
    
    
    1ITEM 1A. RISK FACTORS
    
    
    28ITEM 1B. UNRESOLVED STAFF COMMENTS
    
    
    37ITEM 3. LEGAL PROCEEDINGS
    
    
    37ITEM 4. RESERVED
    
    
    37PART IIITEM 5. MARKET FOR REGISTRANTS COMMON EQUITY, RELATED STOCKHOLDER
MATTERS AND ISSUER PURCHASES OF EQUITY SECURITIES
    
    
    37ITEM 6. SELECTED FINANCIAL DATA
    
    
    40ITEM 7. MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL
CONDITION AND RESULTS OF OPERATIONS
    
    
    42ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK
    
    
    76ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA
    
    
    77ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON
ACCOUNTING AND FINANCIAL DISCLOSURE
    
    
    77ITEM 9A. CONTROLS AND PROCEDURES
    
    
    77ITEM 9B. OTHER INFORMATION
    
    
    78PART IIIITEM 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE
    
    
    79ITEM 11. EXECUTIVE COMPENSATION
    
    
    79ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND
MANAGEMENT AND RELATED STOCKHOLDER MATTERS
    
    
    79ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND
DIRECTOR INDEPENDENCE
    
    
    79ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES
    
    
    79PART IVITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
    
    
    80EX-10.96EX-10.97EX-12.1EX-21.1EX-23.1EX-31.1EX-31.2EX-32.1
  i




---



##### Table of Contents



PART I
 
 ITEMS 1. AND 2. BUSINESS AND PROPERTIES.
 Statements in this Annual Report on Form 10-K, including those in Items 1 and 2, Business and
Properties, and Item 3, Legal Proceedings, that are not historical in nature should be deemed
forward-looking statements that are inherently uncertain. See Forward-Looking Statements in
Managements Discussion and Analysis of Financial Condition and Results of Operations in Item 7
for a discussion of forward-looking statements and of factors that could cause actual outcomes and
results to differ materially from those projected.
 COMPANY OVERVIEW
  www.alonusa.com
  www.sec.gov www.alonusa.com www.alonusa.com
 
    
    Compensation Committee Charter;
    
    Audit Committee Charter;
    
    Corporate Governance Guidelines; and
    
    Code of Business Conduct and Ethics.
 1




---



##### Table of Contents



BUSINESS
   Refining and Unbranded Marketing
  Big Spring Refinery
      2




---



##### Table of Contents



Year Ended December 31,2009
    
    
    2008
    
    
    2007bpd
    
    
    %
    
    
    bpd
    
    
    %
    
    
    bpd
    
    
    %Refinery throughput:Sour crude
    
    
    48,340
    
    
    
    80.8
    
    
    
    31,654
    
    
    
    83.8
    
    
    
    58,607
    
    
    
    86.0Sweet crude
    
    
    9,238
    
    
    
    15.4
    
    
    
    4,270
    
    
    
    11.3
    
    
    
    5,017
    
    
    
    7.4Blendstocks
    
    
    2,292
    
    
    
    3.8
    
    
    
    1,869
    
    
    
    4.9
    
    
    
    4,521
    
    
    
    6.6Total refinery throughput (1)
    
    
    59,870
    
    
    
    100.0
    
    
    
    37,793
    
    
    
    100.0
    
    
    
    68,145
    
    
    
    100.0Refinery production:Gasoline
    
    
    26,826
    
    
    
    45.0
    
    
    
    14,266
    
    
    
    38.4
    
    
    
    32,135
    
    
    
    47.5Diesel/jet
    
    
    19,136
    
    
    
    32.2
    
    
    
    10,439
    
    
    
    28.2
    
    
    
    19,676
    
    
    
    29.1Asphalt
    
    
    5,289
    
    
    
    8.9
    
    
    
    4,850
    
    
    
    13.1
    
    
    
    7,620
    
    
    
    11.3Petrochemicals
    
    
    2,928
    
    
    
    4.9
    
    
    
    1,221
    
    
    
    3.3
    
    
    
    3,980
    
    
    
    5.9Other
    
    
    5,327
    
    
    
    9.0
    
    
    
    6,298
    
    
    
    17.0
    
    
    
    4,190
    
    
    
    6.2Total refinery production (2)
    
    
    59,506
    
    
    
    100.0
    
    
    
    37,074
    
    
    
    100.0
    
    
    
    67,601
    
    
    
    100.0Refinery utilization (3)
    
    
    
    
    
    
    82.3
    %
    
    
    
    
    
    
    52.3
    %
    
    
    
    
    
    
    92.5
    %
 
 (1)
    
    Total refinery throughput represents the total barrels per day of crude oil and blendstock inputs in the
refinery production process.(2)
    
    Total refinery production represents the barrels per day  of various products produced from processing oil
and other refinery feedstocks through the crude unit and other conversion units at our Big
Spring refinery.(3)
    
    Refinery utilization represents average daily crude oil throughput divided by crude oil
capacity, excluding planned periods of downtime for maintenance and turnarounds.  Big Spring Refinery Raw Material Supply
   3




---



##### Table of Contents



Crude Oil Pipelines
  Crude Oil Pipelines
    
    Status
    
    Miles
    
    ConnectionsAmdel
    
    Sunoco Throughput
    
    
    504
    
    
    Midland and NederlandWhite Oil
    
    Sunoco Throughput
    
    
    25
    
    
    Garden City (Amdel) and Big SpringMesa Interconnect
    
    Owned
    
    
    4
    
    
    Mesa pipeline and Big SpringCenturion
    
    Owned (leased to
Centurion)
    
    
    3
    
    
    Centurion pipeline and Big Spring
    Big Spring Refinery Production
 Gasoline
 Distillates
 Asphalt
 4




---



##### Table of Contents



Petrochemical Feedstocks and Other
 Big Spring Refinery Transportation Fuel Marketing
   Unbranded Transportation Fuel Marketing
 Jet Fuel Marketing
 Product Supply Sales
 Big Spring Product Pipelines
  5




---



##### Table of Contents



ExpirationProduct Pipelines
    
    Access
    
    Miles
    
    Connections
    
    DatePlains (1)
    
    Lease
    
    
    38
    
    
    Coahoma and Midland
    
    
    2012Fin-Tex
    
    HEP throughput
    
    
    137
    
    
    Midland and Orla (Holly)
    
    
    2020Holly
    
    Lease
    
    
    133
    
    
    Orla and El Paso
    
    
    2018Trust
    
    HEP throughput
    
    
    332
    
    
    Big Spring/Abilene/Wichita Falls
    
    
    2020Dyess JP-8
    
    HEP throughput
    
    
    2
    
    
    Abilene and Dyess Air Force Base
    
    
    2020River
    
    HEP throughput
    
    
    47
    
    
    Wichita Falls and Duncan (Magellan)
    
    
    2020Carswell
    
    Owned
    
    
    148
    
    
    Abilene and Fort Worth
    
    
    N/A
 
 (1)
    
    The description of the Plains pipeline does not include a 4-mile pipeline that we own
connecting Big Spring and Coahoma, Texas.      Product Terminals
  6




---



##### Table of Contents



WorkingTerminals
    
    Access
    
    Capacity (1)
    
    Supply Source
    
    Mode of DeliveryBig Spring, Texas (2)
    
    Owned
    
    
    331
    
    
    Pipeline/refinery
    
    Pipeline/truckAbilene, Texas
    
    HEP
    
    
    111
    
    
    Pipeline
    
    Pipeline/truckWichita Falls, Texas
    
    HEP
    
    
    189
    
    
    Pipeline
    
    Pipeline/truckDuncan, Oklahoma
    
    Owned (3)
    
    
    154
    
    
    Pipeline
    
    PipelineOrla, Texas
    
    HEP
    
    
    116
    
    
    Pipeline
    
    PipelineSouthlake, Texas
    
    Terminalling
Agreement
    
    
    212
    
    
    Pipeline
    
    TruckTotal
    
    
    
    
    1,113
 
 (1)
    
    Measured in thousands of barrels.(2)
    
    Includes the tankage located at our Big Spring refinery.(3)
    
    The terminal is owned, but the underlying real property is leased.  California Refineries and Terminals
     7




---



##### Table of Contents



Year Ended December 31,2009
    
    2008
    
    2007bpd
    
    %
    
    bpd
    
    %
    
    bpd
    
    %Refinery throughput:Medium sour crude
    
    
    13,408
    
    
    
    43.0
    
    
    
    8,014
    
    
    
    25.8
    
    
    
    20,839
    
    
    
    33.7Heavy crude
    
    
    17,420
    
    
    
    55.9
    
    
    
    22,590
    
    
    
    72.6
    
    
    
    40,700
    
    
    
    65.9Blendstocks
    
    
    330
    
    
    
    1.1
    
    
    
    495
    
    
    
    1.6
    
    
    
    223
    
    
    
    0.4Total refinery throughput (1)
    
    
    31,158
    
    
    
    100.0
    
    
    
    31,099
    
    
    
    100.0
    
    
    
    61,762
    
    
    
    100.0Refinery production:Gasoline
    
    
    4,920
    
    
    
    16.2
    
    
    
    4,141
    
    
    
    13.7
    
    
    
    7,318
    
    
    
    12.1Diesel/jet
    
    
    7,123
    
    
    
    23.5
    
    
    
    7,481
    
    
    
    24.8
    
    
    
    13,360
    
    
    
    22.1Asphalt
    
    
    8,976
    
    
    
    29.5
    
    
    
    9,214
    
    
    
    30.5
    
    
    
    19,006
    
    
    
    31.5Light unfinished
    
    
    117
    
    
    
    0.4
    
    
    
    
    
    
    
    
    
    
    
    3,071
    
    
    
    5.1Heavy unfinished
    
    
    8,813
    
    
    
    29.0
    
    
    
    9,182
    
    
    
    30.4
    
    
    
    16,793
    
    
    
    27.9Other
    
    
    418
    
    
    
    1.4
    
    
    
    192
    
    
    
    0.6
    
    
    
    793
    
    
    
    1.3Total refinery production (2)
    
    
    30,367
    
    
    
    100.0
    
    
    
    30,210
    
    
    
    100.0
    
    
    
    60,341
    
    
    
    100.0Refinery utilization (3)
    
    
    
    
    
    
    46.2
    %
    
    
    
    
    
    
    46.3
    %
    
    
    
    
    
    
    85.9
    %
 
 (1)
    
    Total refinery throughput represents the total barrels per day of crude oil and blendstock inputs in the
refinery production process.(2)
    
    Total refinery production represents the  barrels per day  of various products produced from processing
crude oil and other refinery feedstocks through the crude units and other conversion units at
our California refineries.(3)
    
    Refinery utilization represents average daily crude oil throughput divided by crude oil
capacity, excluding planned periods of downtime for maintenance and turnarounds. Reflects the
effects of downtime associated with a planned turnaround of our No. 2 crude unit at the
Paramount refinery in March and April 2007 and the downtime to optimize our refining and
asphalt economics in 2009 and  2008.  8




---



##### Table of Contents



California Refineries Raw Material Supply
  Crude Oil Pipelines
  Crude Oil Pipelines
    
    Status
    
    Miles
    
    ConnectionsParamount Crude
    
    Owned
    
    
    2.5
    
    
    Paramount and East Hynes TerminalChevron Crude
    
    Third Party
    
    
    15
    
    
    Paramount and local gathering systemNo. 3/No. 4
    
    Owned
    
    
    13
    
    
    Long Beach and Long Beach HarborBP
    
    Third Party
    
    
    1
    
    
    Long Beach and East Hynes TerminalPlains Pipeline
    
    Third Party
    
    
    14
    
    
    Long Beach and West Hynes Terminal
   California Refineries Production
 Gasoline
 Distillates
 9




---



##### Table of Contents



Asphalt
 Light and Heavy Unfinished Feedstocks
 California Refineries Transportation Fuel Marketing
    California Product Pipelines/Terminal
   Product Pipelines
    
    Access
    
    Miles
    
    ConnectionsLine 145
    
    Owned and Leased
    
    8
    
    Paramount to a connection with Line 145Line 166
    
    Leased
    
    2
    
    Connects to Line 145 to City of Carson, California (Kinder Morgan)
  California Feedstock Pipelines
  10




---



##### Table of Contents



Feedstock Pipelines
    
    Terminal
    
    Access
    
    Tankage (1)
    
    Miles
    
    ConnectionsChevron No.1
    
    
    
    Leased
    
    
    
    
    
    
    4
    
    
    Connects our
Paramount and Long
Beach refineries to
our Lakewood
TerminalLakewood
    
    Owned
    
    
    110
    
    
    
    
    
    
    Connects the
Chevron No. 1
pipeline to our
Line 160 pipelineLine 160
    
    
    
    Owned
    
    
    
    
    
    
    7.1
    
    
    Connects the
Lakewood Terminal
to our leased tanks
at Kinder Morgan,
other refiners and
third party
customersKinder Morgan
    
    Leased
    
    
    180
    
    
    
    
    
    
    Connects to our
Black Oil Pipeline
for deliveries to
other refiners and
third party
customersLine 35, L-52, E-12A
    
    
    
    Owned
    
    
    
    
    
    
    4
    
    
    Connects our Long
Beach and Paramount
RefineriesBlack Oil Pipeline
    
    
    
    Owned
    
    
    
    
    
    
    19
    
    
    Connects the Kinder
Morgan Terminal
and Plains
Pipeline System to
LA Basin refiners
and waterborne
terminals
 
 (1)
    
    Measured in thousands of barrels. Krotz Springs Refinery
      11




---



##### Table of Contents



Year Ended December 31, (1)2009
    
    2008bpd
    
    %
    
    bpd
    
    %Refinery throughput:Light sweet crude
    
    
    22,942
    
    
    
    47.5
    
    
    
    43,361
    
    
    
    74.5Heavy sweet crude
    
    
    22,258
    
    
    
    46.0
    
    
    
    11,979
    
    
    
    20.6Blendstocks
    
    
    3,137
    
    
    
    6.5
    
    
    
    2,844
    
    
    
    4.9Total refinery throughput (2)
    
    
    48,337
    
    
    
    100.0
    
    
    
    58,184
    
    
    
    100.0Refinery production:Gasoline
    
    
    22,264
    
    
    
    45.4
    
    
    
    25,195
    
    
    
    42.8Diesel/jet
    
    
    21,318
    
    
    
    43.4
    
    
    
    26,982
    
    
    
    45.9Heavy oils
    
    
    1,238
    
    
    
    2.5
    
    
    
    1,402
    
    
    
    2.4Other
    
    
    4,258
    
    
    
    8.7
    
    
    
    5,258
    
    
    
    8.9Total refinery production (3)
    
    
    49,078
    
    
    
    100.0
    
    
    
    58,837
    
    
    
    100.0Refinery utilization (4)
    
    
    
    
    
    
    65.3
    %
    
    
    
    
    
    
    66.6
    %
 
 (1)
    
    2008 data includes our Krotz Springs refinery for the period from July 1, 2008 through
December 31, 2008.(2)
    
    Total refinery throughput represents the total barrels per day of crude oil and blendstock
inputs in the refinery production process.(3)
    
    Total refinery production represents the barrels per day of various products produced from
processing oil and other refinery feedstocks through the crude unit and other conversion units
at our Krotz Springs refinery.(4)
    
    Refinery utilization represents average daily crude oil throughput divided by crude oil
capacity, excluding planned periods of downtime for maintenance and turnarounds. Refinery
throughput and production for 2009 reflects the effects of downtime associated with a shutdown
that was originally scheduled for the first quarter of 2010 that was accelerated to November
2009. Refinery throughput and production for 2008 reflects the effects of shutdowns during
hurricanes Gustav and Ike and limited crude supply due to widespread electrical outages
following the hurricanes. Krotz Springs Refinery Raw Material Supply
    12




---



##### Table of Contents



Krotz Springs Refinery Production
 Gasoline
 Distillates
 Heavy Oils and Other
 Krotz Springs Refinery Transportation Fuel Marketing
   Krotz Springs Refinery Product Pipeline
   13




---



##### Table of Contents



Asphalt
        14




---



##### Table of Contents



Texas Asphalt Marketing
   West Coast Asphalt Marketing
    Asphalt StorageTerminals
    
    Capacity (1)
    
    Receipt Capabilities
    
    Delivery CapabilitiesCalifornia Refineries
    
    
    731
    
    
    Refinery, Rail, Truck
    
    Rail, TruckWillbridge, OR refinery
    
    
    1,129
    (2)
    
    Refinery, Rail, Truck, Marine
    
    Rail, Truck, MarineElk Grove, CA
    
    
    307
    
    
    Rail, Truck
    
    TruckBakersfield, CA
    
    
    183
    
    
    Rail, Truck
    
    TruckMojave, CA
    
    
    283
    
    
    Rail, Truck
    
    TruckRichmond Beach, WA
    
    
    702
    (2)
    
    Rail, Truck, Marine
    
    Truck, MarineFernley, NV (3)
    
    
    254
    
    
    Rail, Truck
    
    TruckPhoenix, AZ
    
    
    165
    
    
    Rail, Truck
    
    TruckFlagstaff, AZ
    
    
    25
    
    
    Rail, Truck
    
    TruckFredonia, AZ
    
    
    79
    
    
    Truck
    
    Truck
 
 (1)
    
    Measured in thousands of barrels.(2)
    
    Storage figures for Willbridge and Richmond Beach include tanks in service for storage of
crude oil, fuel oil or other products.(3)
    
    50% interest. 15




---



##### Table of Contents



Retail and Branded Marketing
  Retail
    Location
    
    Owned
    
    Leased
    
    TotalBig Spring, Texas
    
    
    6
    
    
    
    1
    
    
    
    7El Paso, Texas
    
    
    13
    
    
    
    73
    
    
    
    86Lubbock, Texas
    
    
    17
    
    
    
    5
    
    
    
    22Midland, Texas
    
    
    9
    
    
    
    9
    
    
    
    18Odessa, Texas
    
    
    11
    
    
    
    25
    
    
    
    36Wichita Falls, Texas
    
    
    8
    
    
    
    4
    
    
    
    12Abilene, Texas
    
    
    34
    
    
    
    9
    
    
    
    43Waco, Texas
    
    
    11
    
    
    
    3
    
    
    
    14Albuquerque, New Mexico
    
    
    12
    
    
    
    11
    
    
    
    23Other
    
    
    29
    
    
    
    18
    
    
    
    47Total stores
    
    
    150
    
    
    
    158
    
    
    
    308
  16




---



##### Table of Contents



Convenience Store Management and Employees
 Distribution and Supply
 7-Eleven License Agreement
 Technology and Store Automation
 Branded Marketing
   Distribution Network and Distributor Arrangements.
 17




---



##### Table of Contents



FINA Brand Sub-Licensing.
 FINA Minimum Standards Program.
 Payment Card Processing.
 Technology.
 Competition
    18




---



##### Table of Contents



19




---



##### Table of Contents



Government Regulation and Legislation
 Environmental Controls and Expenditures
  Environmental Expenditures
    20




---



##### Table of Contents



21




---



##### Table of Contents



Remediation Efforts
   22




---



##### Table of Contents



Environmental Indemnity from FINA
 Environmental Insurance
 Environmental Indemnity to HEP
 23




---



##### Table of Contents



Environmental Indemnity to Sunoco
 Other Government Regulation
     24




---



##### Table of Contents



Employees
   Properties
  Executive Officers of the Registrant
  Name
    
    Age
    
    PositionDavid Wiessman
    
    
    55
    
    
    Executive Chairman of the Board of DirectorsJeff D. Morris
    
    
    58
    
    
    Director and Chief Executive OfficerPaul Eisman
    
    
    54
    
    
    PresidentShai Even
    
    
    41
    
    
    Senior Vice President and Chief Financial OfficerJoseph Israel
    
    
    38
    
    
    Chief Operating OfficerClaire A. Hart
    
    
    54
    
    
    Senior Vice PresidentJoseph A. Concienne
    
    
    59
    
    
    Senior Vice President of RefiningAlan Moret
    
    
    55
    
    
    Senior Vice President of SupplyHarlin R. Dean
    
    
    43
    
    
    Senior Vice President  Legal, General Counsel and SecretaryMichael Oster
    
    
    38
    
    
    Senior Vice President of Mergers and AcquisitionsJimmy C. Crosby*
    
    
    50
    
    
    Vice President of Refining  Big SpringEd Juno*
    
    
    57
    
    
    Vice President of Refining  ParamountWilliam Wuensche*
    
    
    49
    
    
    Vice President of Refining  Krotz SpringsWilliam L. Thorpe*
    
    
    63
    
    
    Vice President of Asphalt OperationsKyle McKeen*
    
    
    46
    
    
    President and Chief Executive Officer of Alon BrandsJoseph Lipman*
    
    
    64
    
    
    President and Chief Executive Officer of SCS
  David Wiessman
 25




---



##### Table of Contents



Jeff D. Morris
 Paul Eisman
 Shai Even
 Joseph Israel
 Claire A. Hart
 Joseph A. Concienne
 Alan Moret
 Harlin R. Dean
 26




---



##### Table of Contents



Michael Oster
 Jimmy C. Crosby
 Ed Juno
 William Wuensche
 William L. Thorpe
 Kyle McKeen
 Joseph Lipman
 27




---



##### Table of Contents



ITEM 1A. RISK FACTORS.
  The price volatility of crude oil, other feedstocks, refined products and fuel and utility services
may have a material adverse effect on our earnings, profitability and cash flows.
  
    
    changes in global and local economic conditions;
    
    domestic and foreign demand for fuel products;
    
    worldwide political conditions, particularly in significant oil producing regions
such as the Middle East, West Africa and Venezuela;
    
    the level of foreign and domestic production of crude oil and refined products and
the level of crude oil, feedstock and refined products imported into the United
States;
    
    utilization rates of U.S. refineries;
    
    development and marketing of alternative and competing fuels;
    
    commodities speculation;
    
    accidents, interruptions in transportation, inclement weather or other events that
can cause unscheduled shutdowns or otherwise adversely affect our refineries;
    
    federal and state government regulations; and
    
    local factors, including market conditions, weather conditions and the level of
operations of other refineries and pipelines in our markets.
   28




---



##### Table of Contents



Our profitability depends, in part, on the sweet/sour crude oil price spread. A decrease in this
spread could negatively affect our profitability.
  The profitability of our California refineries depends, in part, on the light/heavy crude oil price
spread. A decrease in this spread could negatively affect our profitability.
  The dangers inherent in our operations could cause disruptions and could expose us to potentially
significant losses, costs or liabilities.
   We are subject to interruptions of supply as a result of our reliance on pipelines for
transportation of crude oil and refined products.
  29




---



##### Table of Contents



If the price of crude oil increases significantly, it could reduce our profit on our fixed-price
asphalt supply contracts.
  Our operating results are seasonal and generally lower in the first and fourth quarters of the
year.
  If the price of crude oil increases significantly, it could limit our ability to purchase enough
crude oil to operate our refineries at full capacity.
  Changes in our credit profile could affect our relationships with our suppliers, which could have a
material adverse effect on our liquidity and our ability to operate our refineries at full
capacity.
  Competition in the refining and marketing industry is intense, and an increase in competition in
the markets in which we sell our products could adversely affect our earnings and profitability.
   30




---



##### Table of Contents



Our indebtedness could adversely affect our financial condition or make us more vulnerable to
adverse economic conditions.
  
    
    we may be limited in our ability to obtain additional financing to fund our working
capital needs, capital expenditures and debt service requirements or our other operational
needs;
    
    we may be limited in our ability to use operating cash flow in other areas of our
business because we must dedicate a substantial portion of these funds to make principal
and interest payments on our debt;
    
    we may be at a competitive disadvantage compared to competitors with less leverage
since we may be less capable of responding to adverse economic and industry conditions; and
    
    we may not have sufficient flexibility to react to adverse changes in the economy, our
business or the industries in which we operate.
  Competition in the asphalt industry is intense, and an increase in competition in the markets in
which we sell our asphalt products could adversely affect our earnings and profitability.
   Competition in the retail industry is intense, and an increase in competition in the markets in
which our retail businesses operate could adversely affect our earnings and profitability.
  31




---



##### Table of Contents



We may incur significant costs to comply with new or changing environmental laws and regulations.
    The adoption of climate change legislation by Congress or the regulation of greenhouse gas
emissions by the United States Environmental Protection Agency (EPA) could result in increased
operating costs, lower profitability and reduced demand for our refined products.
   32




---



##### Table of Contents



We may incur significant costs and liabilities with respect to environmental lawsuits and
proceedings and any investigation and remediation of existing and future environmental conditions.
  33




---



##### Table of Contents



We could incur substantial costs or disruptions in our business if we cannot obtain or maintain
necessary permits and authorizations or otherwise comply with health, safety, environmental and
other laws and regulations.
  We could encounter significant opposition to operations at our California refineries.
  The occurrence of a release of hazardous materials or a catastrophic event affecting our California
refineries could endanger persons living nearby.
  Certain of our facilities are located in areas that have a history of earthquakes or hurricanes,
the occurrence of which could materially impact our operations.
  Terrorist attacks, threats of war or actual war may negatively affect our operations, financial
condition, results of operations and prospects.
  34




---



##### Table of Contents



Covenants in our credit agreements could limit our ability to undertake certain types of
transactions and adversely affect our liquidity.
  Our insurance policies do not cover all losses, costs or liabilities that we may experience.
  We are exposed to risks associated with the credit-worthiness of the insurer of our environmental
policies.
  If we lose any of our key personnel, our ability to manage our business and continue our growth
could be negatively affected.
  A substantial portion of our Big Spring refinerys workforce is unionized, and we may face labor
disruptions that would interfere with our operations.
  35




---



##### Table of Contents



We conduct our convenience store business under a license agreement with 7-Eleven, and the
loss of this license could adversely affect the results of operations of our retail and branded
marketing segment.
  We may not be able to successfully execute our strategy of growth through acquisitions.
  
    
    diversion of management time and attention from our existing business;
    
    challenges in managing the increased scope, geographic diversity and complexity of
operations;
    
    difficulties in integrating the financial, technological and management standards,
processes, procedures and controls of an acquired business with those of our existing
operations;
    
    liability for known or unknown environmental conditions or other contingent liabilities
not covered by indemnification or insurance;
    
    greater than anticipated expenditures required for compliance with environmental or
other regulatory standards or for investments to improve operating results;
    
    difficulties in achieving anticipated operational improvements;
    
    incurrence of additional indebtedness to finance acquisitions or capital expenditures
relating to acquired assets; and
    
    issuance of additional equity, which could result in further dilution of the ownership
interest of existing stockholders.
  We depend upon our subsidiaries for cash to meet our obligations and pay any dividends, and we do
not own 100% of the stock of our operating subsidiaries.
   36




---



##### Table of Contents



It may be difficult to serve process on or enforce a United States judgment against certain of our
directors.
  
 ITEM 1B. UNRESOLVED STAFF COMMENTS.
  
 ITEM 3. LEGAL PROCEEDINGS.
  
 ITEM 4. RESERVED.
 
 PART II
 
 ITEM 5. MARKET FOR REGISTRANTS COMMON EQUITY, RELATED STOCKHOLDER MATTERS AND ISSUER PURCHASES OF
EQUITY SECURITIES.
 Market Information
   Quarterly Period
    
    High
    
    Low2009Fourth Quarter
    
    $
    10.18
    
    
    $
    6.60Third Quarter
    
    
    11.20
    
    
    
    8.20Second Quarter
    
    
    15.90
    
    
    
    9.92First Quarter
    
    
    15.46
    
    
    
    8.762008Fourth Quarter
    
    $
    14.91
    
    
    $
    6.19Third Quarter
    
    
    17.00
    
    
    
    7.31Second Quarter
    
    
    17.85
    
    
    
    11.31First Quarter
    
    
    27.88
    
    
    
    11.62
 37




---



##### Table of Contents



Holders
  Dividends
          Recent Sales of Unregistered Securities
  Purchases of Equity Securities by the Issuer and Affiliated Purchasers
  38




---



##### Table of Contents



Stockholder Return Performance Graph
  
 39




---



##### Table of Contents



ITEM 6. SELECTED FINANCIAL DATA.
    Year Ended December 31,2009
    
    
    2008
    
    
    2007
    
    
    2006
    
    
    2005(dollars in thousands, except per share data)STATEMENT OF OPERATIONS DATA:Net sales (1)
    
    $
    3,915,732
    
    
    $
    5,156,706
    
    
    $
    4,542,151
    
    
    $
    3,093,890
    
    
    $
    2,330,334Operating costs and expenses (1)
    
    
    3,994,977
    
    
    
    5,258,153
    
    
    
    4,363,238
    
    
    
    2,877,811
    
    
    
    2,180,162Gain on involuntary conversion of assets (2)
    
    
    
    
    
    
    279,680
    
    
    
    
    
    
    
    
    
    
    
    Gain (loss) on disposition of assets (3)
    
    
    (1,591
    )
    
    
    45,244
    
    
    
    7,206
    
    
    
    63,255
    
    
    
    38,591Operating income (loss)
    
    
    (80,836
    )
    
    
    223,477
    
    
    
    186,119
    
    
    
    279,334
    
    
    
    188,763Net income (loss) available to common
stockholders
    
    
    (115,156
    )
    
    
    82,883
    
    
    
    103,936
    
    
    
    157,368
    
    
    
    103,988Earnings (loss) per share, basic (4)
    
    $
    (2.46
    )
    
    $
    1.77
    
    
    $
    2.22
    
    
    $
    3.37
    
    
    $
    2.61Weighted average shares outstanding, basic (4)
    
    
    46,829
    
    
    
    46,788
    
    
    
    46,763
    
    
    
    46,738
    
    
    
    39,889Earnings (loss) per share, diluted
    
    $
    (2.46
    )
    
    $
    1.72
    
    
    $
    2.16
    
    
    $
    3.36
    
    
    $
    2.61Weighted average shares outstanding, diluted
    
    
    46,829
    
    
    
    49,583
    
    
    
    46,804
    
    
    
    46,779
    
    
    
    39,908Cash dividends per common share
    
    
    0.16
    
    
    
    0.16
    
    
    
    0.16
    
    
    
    3.03
    
    
    
    1.96CASH FLOW DATA:Net cash provided by (used in):Operating activities
    
    $
    283,145
    
    
    $
    (812
    )
    
    $
    123,950
    
    
    $
    142,977
    
    
    $
    137,895Investing activities
    
    
    (138,691
    )
    
    
    (610,322
    )
    
    
    (147,254
    )
    
    
    (421,070
    )
    
    
    (106,962
    )Financing activities
    
    
    (122,471
    )
    
    
    560,973
    
    
    
    27,753
    
    
    
    205,439
    
    
    
    42,530BALANCE SHEET DATA (end of period):Cash and cash equivalents and short-term
investments
    
    $
    40,437
    
    
    $
    18,454
    
    
    $
    95,911
    
    
    $
    64,166
    
    
    $
    322,140Working capital
    
    
    84,257
    
    
    
    250,384
    
    
    
    279,580
    
    
    
    228,779
    
    
    
    275,996Total assets
    
    
    2,132,789
    
    
    
    2,413,433
    
    
    
    1,581,386
    
    
    
    1,408,785
    
    
    
    758,780Total debt
    
    
    937,024
    
    
    
    1,103,569
    
    
    
    536,615
    
    
    
    498,669
    
    
    
    132,390Total equity
    
    
    431,918
    
    
    
    536,867
    
    
    
    403,922
    
    
    
    299,862
    
    
    
    286,559
 
 (1)
    
    Our buy/sell arrangements involve linked purchases and sales related to refined product
contracts entered into to address location, quality or grade requirements. As of January 1,
2006, these buy/sell transactions are included on a net basis in sales in the consolidated
statements of operations and profits are recognized when the exchanged product is sold. Prior
to January 1, 2006, the results of these buy/sell transactions were recorded separately in
sales and cost of sales in the consolidated statements of operations. See Note 2 to our
consolidated financial statements included elsewhere in this Annual Report on Form 10-K.(2)
    
    Gain on involuntary conversion of assets reported in 2008 of $279.7 million represents the
insurance proceeds received as a result of the Big Spring refinery fire in excess of the book
value of the assets impaired of $25.3 million and demolition and repair expenses of $25.0
million incurred through December 31, 2008. 40




---



##### Table of Contents



(3)
    
    Gain on disposition of assets reported in 2008 primarily reflects the recognition of all the
remaining deferred gain associated with the HEP transaction due to the termination of an
indemnification agreement with HEP. Gain on disposition of assets reported in 2007 reflects
the recognition of $7.2 million deferred gain recorded primarily in connection with the HEP
transaction. Gain on disposition of assets reported in 2006 reflects the $52.5 million gain
recognized in connection with the Amdel and White Oil transaction and the recognition of $10.8
million deferred gain recorded in connection with the HEP transaction. Gain on disposition of
assets reported in 2005 reflect the initial gain recognized in connection with the assets
contributed in the HEP transaction.(4)
    
    Basic weighted average shares outstanding and basic earnings per share amounts for the
periods presented reflect the effect of a 33,600-for-one split of our common stock which was
effected on July 6, 2005. On August 2, 2005, we completed an initial public offering of
11,730,000 shares of our common stock. The shares issued in our initial public offering are
included in the number of weighted average shares outstanding at December 31, 2009, 2008, 2007
and 2006, respectively. 41




---



##### Table of Contents



ITEM 7. MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS.
 The following discussion of our financial condition and results of operations is provided as a
supplement to, and should be read in conjunction with, our consolidated financial statements and
the notes thereto included elsewhere in this Annual Report on Form 10-K and the other sections of
this Annual Report on Form 10-K , including Items 1 and 2 Business and Properties, and Item 6
Selected Financial Data.
 Forward-Looking Statements
    
    
    changes in general economic conditions and capital markets;
    
    changes in the underlying demand for our products;
    
    the availability, costs and price volatility of crude oil, other refinery feedstocks
and refined products;
    
    changes in the sweet/sour spread;
    
    changes in the light/heavy spread;
    
    the effects of transactions involving forward contracts and derivative instruments;
    
    actions of customers and competitors;
    
    changes in fuel and utility costs incurred by our facilities;
    
    disruptions due to equipment interruption, pipeline disruptions or failure at our or
third-party facilities;
    
    the execution of planned capital projects;
    
    adverse changes in the credit ratings assigned to our trade credit and debt
instruments;
    
    the effects of and cost of compliance with current and future state and federal
environmental, economic, safety and other laws, policies and regulations;
    
    operating hazards, natural disasters, casualty losses and other matters beyond our
control;
 42




---



##### Table of Contents




    
    our planned project of the design and construction of a hydrocracker unit at our
California refineries may not be completed within the expected time frame or within the
budgeted costs for such project due to factors outside of our control;
    
    the global financial crisis impact on our business and financial condition in ways
that we currently cannot predict. We may face significant challenges if conditions in the
financial markets do not improve or continue to worsen, such as adversely impacting our
ability to refinance existing credit facilities or extend their terms; and
    
    the other factors discussed in our Annual Report on Form 10-K for the year ended
December 31, 2009 under the caption Risk Factors.
  Overview
   Refining and Unbranded Marketing Segment
    43




---



##### Table of Contents



Asphalt Segment
 Retail and Branded Marketing Segment
  Summary of 2009 Developments
    44




---



##### Table of Contents



2009 Operations Highlights
  
    
    Operating loss was ($80.8) million, compared to operating income of $223.5 million
in 2008. Operating income decreased by $304.3 million for 2009 compared to 2008. The year
2008 included gains of $279.7 million on the involuntary conversion of assets due to the
Big Spring refinery fire, and $45.2 million for the gain on disposition of assets.
    
    The Big Spring refinery and California refineries combined throughput for the year
ended December 31, 2009 averaged 91,028 bpd, consisting of 59,870 bpd at the Big Spring
refinery and 31,158 bpd at the California refineries compared to a combined average of
68,892 bpd for the same period last year, consisting of 37,793 bpd at the Big Spring
refinery and 31,099 bpd at the California refineries. The Big Spring refinery had higher
throughput for the year ended December 31, 2009, compared to the same period last year
primarily due to the 2008 fire at the Big Spring refinery. The Krotz Springs refinery
throughput for the year ended December 31, 2009, averaged 48,337 bpd and for the period
from its acquisition effective July 1, 2008 through December 31, 2008, averaged 58,184 bpd.
The lower throughput in 2009 is due to a turnaround that began in November 2009.
    
    Refinery operating margin at the Big Spring refinery was $4.35 per barrel for the
year ended December 31, 2009, compared to ($3.18) per barrel for the same period in 2008.
This increase was primarily due to the depressed margins experienced in conjunction with
the fire at the Big Spring refinery in 2008. The Big Spring refinery light product yields
were approximately 82% for the year ended December 31, 2009, compared to 70% for the same
period in 2008. Refinery operating margin at the California refineries was $1.80 per
barrel for the year ended December 31, 2009, compared to $1.65 per barrel for the same
period in 2008. The Krotz Springs refinery operating margin for the year ended December
31, 2009, was $5.66 per barrel compared to $7.25 per barrel for the period from its
acquisition effective July 1, 2008 through December 31, 2008. The lower Krotz Springs
refinery operating margin is due primarily to lower Gulf Coast 2/1/1 high sulfur diesel
margins in 2009.
    
    Gulf coast 3/2/1 average crack spreads were $7.24 per barrel for the year ended
December 31, 2009, compared to $10.47 per barrel for the same period in 2008. Gulf Coast
2/1/1 high sulfur diesel average crack spreads for the year ended December 31, 2009, was
$6.50 per barrel compared to $11.28 per barrel for the same period in 2008. West Coast
3/2/1 average crack spreads for the year ended December 31, 2009, was $13.92 per barrel
compared to $15.80 per barrel for the same period in 2008.
 45




---



##### Table of Contents




    
    The average sweet/sour spread for the year ended December 31, 2009 was $1.52 per barrel
compared to $3.78 per barrel for 2008. The average light/heavy spread for the year ended
December 31, 2009, was $5.46 per barrel compared to $15.63 per barrel for 2008.
    
    Asphalt margins in 2009 averaged $46.07 per ton compared to an average of $113.43
per ton in 2008. The average blended asphalt sales price decreased 19.9% from $511.95 per
ton for the year ended December 31, 2008, to $409.88 per ton for the year ended December
31, 2009, and the average non-blended asphalt sales price decreased 46.1% from $315.48 per
ton for the year ended December 31, 2008 to $170.05 per ton for the year ended December 31,
2009. The blended asphalt sales accounted for 92% of total asphalt sales for the year
ended December 31, 2009. The decrease in the blended asphalt sales price of 19.9% was less
than the 37.9% decrease in WTI prices for the year ended December 31, 2009.
    
    In our retail and branded marketing segment, retail fuel sales gallons increased by
24.4% from 97.0 million gallons for the year ended December 31, 2008, to 120.7 million
gallons for the year ended December 31, 2009. Our integrated branded fuel sales increased
by 15.6% from 225.5 million gallons for the year ended December 31, 2008, to 260.6 million
gallons for the year ended December 31, 2009.
 Major Influences on Results of Operations
 Refining and Unbranded Marketing
    46




---



##### Table of Contents



Asphalt
 Retail and Branded Marketing
 47




---



##### Table of Contents



Factors Affecting Comparability
  Big Spring Refinery Fire
    Retail Store Acquisitions
  Refinery Acquisitions
  48




---



##### Table of Contents



Unscheduled Turnaround and Reduced Crude Oil Throughput
    Hurricane Activity
  HEP Transaction
  Results of Operations
 Net Sales
  Cost of Sales
 Direct Operating Expenses
 Selling, General and Administrative Expenses
 49




---



##### Table of Contents



Summary Financial Tables
 50




---



##### Table of Contents



ALON USA ENERGY, INC. CONSOLIDATED
 Year Ended December 31,2009
    
    
    2008
    
    
    2007(dollars in thousands, except per share data)STATEMENT OF OPERATIONS DATA:Net sales (1)
    
    $
    3,915,732
    
    
    $
    5,156,706
    
    
    $
    4,542,151Operating costs and expenses:Cost of sales
    
    
    3,502,782
    
    
    
    4,853,195
    
    
    
    3,999,287Direct operating expenses
    
    
    265,502
    
    
    
    216,498
    
    
    
    201,196Selling, general and administrative expenses (2)
    
    
    129,446
    
    
    
    119,852
    
    
    
    105,352Net costs associated with fire (3)
    
    
    
    
    
    
    56,854
    
    
    
    Business interruption recovery (4)
    
    
    
    
    
    
    (55,000
    )
    
    
    Depreciation and amortization (5)
    
    
    97,247
    
    
    
    66,754
    
    
    
    57,403Total operating costs and expenses
    
    
    3,994,977
    
    
    
    5,258,153
    
    
    
    4,363,238Gain on involuntary conversion of assets (6)
    
    
    
    
    
    
    279,680
    
    
    
    Gain (loss) on disposition of assets (7)
    
    
    (1,591
    )
    
    
    45,244
    
    
    
    7,206Operating income (loss)
    
    
    (80,836
    )
    
    
    223,477
    
    
    
    186,119Interest expense (8)
    
    
    (111,137
    )
    
    
    (67,550
    )
    
    
    (47,747
    )Equity earnings (losses) of investees
    
    
    24,558
    
    
    
    (1,522
    )
    
    
    11,177Other income, net
    
    
    331
    
    
    
    1,500
    
    
    
    6,565Income (loss) before income tax expense (benefit),
non-controlling interest in income (loss) of subsidiaries
and accumulated dividends on preferred stock of subsidiary
    
    
    (167,084
    )
    
    
    155,905
    
    
    
    156,114Income tax expense (benefit)
    
    
    (64,877
    )
    
    
    62,781
    
    
    
    46,199Income (loss) before non-controlling interest in income
(loss) of subsidiaries and accumulated dividends on
preferred stock of subsidiary
    
    
    (102,207
    )
    
    
    93,124
    
    
    
    109,915Non-controlling interest in income (loss) of subsidiaries
    
    
    (8,551
    )
    
    
    5,941
    
    
    
    5,979Accumulated dividends on preferred stock of subsidiary (9)
    
    
    21,500
    
    
    
    4,300
    
    
    
    Net income (loss) available to common stockholders
    
    $
    (115,156
    )
    
    $
    82,883
    
    
    $
    103,936Earnings (loss) per share, basic
    
    $
    (2.46
    )
    
    $
    1.77
    
    
    $
    2.22Weighted average shares outstanding, basic (in thousands)
    
    
    46,829
    
    
    
    46,788
    
    
    
    46,763Earnings (loss) per share, diluted
    
    $
    (2.46
    )
    
    $
    1.72
    
    
    $
    2.16Weighted average shares outstanding, diluted (in thousands)
    
    
    46,829
    
    
    
    49,583
    
    
    
    46,804Cash dividends per share
    
    $
    0.16
    
    
    $
    0.16
    
    
    $
    0.16CASH FLOW DATA:Net cash provided by (used in):Operating activities
    
    $
    283,145
    
    
    $
    (812
    )
    
    $
    123,950Investing activities
    
    
    (138,691
    )
    
    
    (610,322
    )
    
    
    (147,254
    )Financing activities
    
    
    (122,471
    )
    
    
    560,973
    
    
    
    27,753BALANCE SHEET DATA (end of period):Cash and cash equivalents and short-term investments
    
    $
    40,437
    
    
    $
    18,454
    
    
    $
    95,911Working capital
    
    
    84,257
    
    
    
    250,384
    
    
    
    279,580Total assets
    
    
    2,132,789
    
    
    
    2,413,433
    
    
    
    1,581,386Total debt
    
    
    937,024
    
    
    
    1,103,569
    
    
    
    536,615Total stockholders equity
    
    
    422,772
    
    
    
    434,651
    
    
    
    388,202Non-controlling interest in subsidiaries and preferred
stock of subsidiary including accumulated dividends
    
    
    9,146
    
    
    
    102,216
    
    
    
    15,720Total equity
    
    
    431,918
    
    
    
    536,867
    
    
    
    403,922OTHER DATA:Adjusted EBITDA (10)
    
    $
    42,891
    
    
    $
    244,965
    
    
    $
    254,058Capital expenditures (11)
    
    
    81,660
    
    
    
    62,356
    
    
    
    42,204Capital expenditures to rebuild the Big Spring refinery
    
    
    46,769
    
    
    
    362,178
    
    
    
    Capital expenditures for turnaround and chemical catalyst
    
    
    24,699
    
    
    
    9,958
    
    
    
    9,842
 51




---



##### Table of Contents



(1)
    
    Includes excise taxes on sales by the retail and branded marketing segment of $47.1 million,
$37.5 million, and $35.8 million for the years ended December 31, 2009, 2008 and 2007,
respectively.(2)
    
    Includes corporate headquarters selling, general and administrative expenses of $0.8 million,
$0.6 million and $0.5 million for the years ended December 31, 2009, 2008 and 2007,
respectively, which are not allocated to our three operating segments.(3)
    
    Includes $51.1 million of expenses incurred from pipeline commitment deficiencies, crude sale
losses and other incremental costs; $5.0 million for our third party liability insurance
deductible under the insurance policy; and depreciation for the temporarily idled facilities
of $0.8 million for the year ended December 31, 2008.(4)
    
    Business interruption recovery of $55.0 million was recorded for the year ended December 31,
2008 as a result of the Big Spring refinery fire with all insurance proceeds received in 2008
and January 2009.(5)
    
    Includes corporate depreciation and amortization of $0.7 million, $0.9 million and $0.9
million for the years ended December 31, 2009, 2008 and 2007, respectively, which are not
allocated to our three operating segments.(6)
    
    A gain on involuntary conversion of assets of $279.7 million has been recorded for the
insurance proceeds received in excess of the book value of the assets impaired of $25.3
million and demolition and repair expenses of $25.0 million incurred through December 31, 2008
as a result of the Big Spring refinery fire.(7)
    
    Gain on disposition of assets reported in 2008 primarily includes the recognition of deferred
gain recorded in connection with the contribution of certain product pipelines and terminals
to Holly Energy Partners, LP, (HEP), in March 2005 (HEP transaction). A recognized gain of
$42.9 million in 2008 represented all the remaining deferred gain associated with the HEP
transaction and was due to the termination of an indemnification agreement with HEP. Gain on
disposition of assets reported in 2007 reflects the recognition of $7.2 million deferred gain
recorded primarily in connection with the HEP transaction.(8)
    
    Interest expense for the year ended December 31, 2009 includes $20.5 million of unamortized
debt issuance costs written off as a result of prepayments of $163.8 million of term debt in
October 2009. Interest expense for 2009 also includes $5.7 million related to the liquidation
of the heating oil hedge in the second quarter of 2009.(9)
    
    Accumulated dividends on preferred stock of subsidiary for year ended December 31, 2009,
represent dividends of $12.9 million for the conversion of the preferred stock into Alon
common stock. Also included for the year ended December 31, 2009 is $8.6 million of
accumulated dividends through December 31, 2009.(10)
    
    See  Reconciliation of Amounts Reported Under Generally Accepted Accounting Principles
for information regarding our definition of Adjusted EBITDA, its limitations as an analytical
tool and a reconciliation of net income to Adjusted EBITDA for the periods presented.(11)
    
    Includes corporate capital expenditures of $3.7 million, $1.2 million and $1.6 million for
the years ended December 31, 2009, 2008 and 2007, respectively, which are not allocated to our
three operating segments. 52




---



##### Table of Contents



REFINING AND UNBRANDED MARKETING SEGMENT (A)
 Year Ended December 31,2009
    
    
    2008
    
    
    2007(dollars in thousands, except per barrel data andpricing statistics)STATEMENT OF OPERATIONS DATA:Net sales (1)
    
    $
    3,359,043
    
    
    $
    4,551,769
    
    
    $
    4,090,607Operating costs and expenses:Cost of sales
    
    
    3,117,528
    
    
    
    4,505,094
    
    
    
    3,714,227Direct operating expenses
    
    
    221,378
    
    
    
    173,142
    
    
    
    154,267Selling, general and administrative expenses
    
    
    29,376
    
    
    
    17,784
    
    
    
    20,071Net costs associated with fire (2)
    
    
    
    
    
    
    56,854
    
    
    
    Business interruption recovery (3)
    
    
    
    
    
    
    (55,000
    )
    
    
    Depreciation and amortization
    
    
    76,252
    
    
    
    50,047
    
    
    
    44,107Total operating costs and expenses
    
    
    3,444,534
    
    
    
    4,747,921
    
    
    
    3,932,672Gain (loss) on involuntary conversion of assets (4)
    
    
    
    
    
    
    279,680
    
    
    
    Gain (loss) on disposition of assets (5)
    
    
    (1,042
    )
    
    
    45,244
    
    
    
    7,138Operating income (loss)
    
    $
    (86,533
    )
    
    $
    128,772
    
    
    $
    165,073KEY OPERATING STATISTICS AND OTHER DATA:Total sales volume (bpd)
    
    
    127,400
    
    
    
    119,195
    
    
    
    91,027Per barrel of throughput:Refinery operating margin  Big Spring (6)
    
    $
    4.35
    
    
    $
    (3.18
    )
    
    $
    12.83Refinery operating margin  CA Refineries (6)
    
    
    1.80
    
    
    
    1.65
    
    
    
    2.73Refinery operating margin  Krotz Springs (6)
    
    
    5.66
    
    
    
    7.25
    
    
    
    N/ARefinery direct operating expense  Big Spring (7)
    
    
    4.21
    
    
    
    4.40
    
    
    
    3.67Refinery direct operating expense  CA Refineries (7)
    
    
    4.82
    
    
    
    5.81
    
    
    
    2.79Refinery direct operating expense  Krotz Springs (7)
    
    
    4.22
    
    
    
    4.30
    
    
    
    N/ACapital expenditures
    
    
    71,555
    
    
    
    57,576
    
    
    
    28,669Capital expenditures to rebuild the Big Spring refinery
    
    
    46,769
    
    
    
    362,178
    
    
    
    Capital expenditures for turnaround and chemical catalyst
    
    
    24,699
    
    
    
    9,958
    
    
    
    9,842PRICING STATISTICS:WTI crude oil (per barrel)
    
    $
    61.82
    
    
    $
    99.56
    
    
    $
    72.32WTS crude oil (per barrel)
    
    
    60.30
    
    
    
    95.78
    
    
    
    67.32MAYA crude oil (per barrel)
    
    
    56.36
    
    
    
    83.93
    
    
    
    59.86Crack spreads (3/2/1) (per barrel):Gulf Coast
    
    $
    7.24
    
    
    $
    10.47
    
    
    $
    15.00Group III
    
    
    8.10
    
    
    
    11.15
    
    
    
    19.41West Coast
    
    
    13.92
    
    
    
    15.80
    
    
    
    27.37Crack spreads (6/1/2/3) (per barrel):West Coast
    
    $
    4.15
    
    
    $
    0.48
    
    
    $
    6.33Crack spreads (2/1/1) (per barrel):Gulf Coast high sulfur diesel
    
    $
    6.50
    
    
    $
    11.28
    
    
    $
    12.80Crude oil differentials (per barrel):WTI less WTS
    
    $
    1.52
    
    
    $
    3.78
    
    
    $
    5.00WTI less MAYA
    
    
    5.46
    
    
    
    15.63
    
    
    
    12.46Product price (per gallon):Gulf Coast unleaded gasoline
    
    
    163.5
    ¢
    
    
    247.1
    ¢
    
    
    204.5
    ¢Gulf Coast ultra low-sulfur diesel
    
    
    166.4
    
    
    
    291.8
    
    
    
    214.7Gulf Coast high sulfur diesel
    
    
    161.9
    
    
    
    280.8
    
    
    
    200.8Group III unleaded gasoline
    
    
    166.2
    
    
    
    248.1
    
    
    
    216.0Group III ultra low-sulfur diesel
    
    
    167.0
    
    
    
    294.5
    
    
    
    223.3West Coast LA CARBOB (unleaded gasoline)
    
    
    185.2
    
    
    
    267.9
    
    
    
    244.2West Coast LA ultra low-sulfur diesel
    
    
    170.6
    
    
    
    288.3
    
    
    
    223.7Natural gas (per MMBTU)
    
    $
    4.16
    
    
    $
    8.90
    
    
    $
    7.12
 
 (A)
    
    In the first quarter of 2008, our branded marketing business was removed from the refining
and marketing segment and combined with the retail segment. Information for 2007 has been
recast to provide a comparison to 2009 and 2008 results. 53




---



##### Table of Contents



Year Ended December 31,THROUGHPUT AND PRODUCTION DATA:
    
    2009
    
    2008
    
    2007Big Spring refinery
    
    bpd
    
    %
    
    bpd
    
    %
    
    bpd
    
    %Refinery throughput:Sour crude
    
    
    48,340
    
    
    
    80.8
    
    
    
    31,654
    
    
    
    83.8
    
    
    
    58,607
    
    
    
    86.0Sweet crude
    
    
    9,238
    
    
    
    15.4
    
    
    
    4,270
    
    
    
    11.3
    
    
    
    5,017
    
    
    
    7.4Blendstocks
    
    
    2,292
    
    
    
    3.8
    
    
    
    1,869
    
    
    
    4.9
    
    
    
    4,521
    
    
    
    6.6Total refinery throughput (8)
    
    
    59,870
    
    
    
    100.0
    
    
    
    37,793
    
    
    
    100.0
    
    
    
    68,145
    
    
    
    100.0Refinery production:Gasoline
    
    
    26,826
    
    
    
    45.0
    
    
    
    14,266
    
    
    
    38.4
    
    
    
    32,135
    
    
    
    47.5Diesel/jet
    
    
    19,136
    
    
    
    32.2
    
    
    
    10,439
    
    
    
    28.2
    
    
    
    19,676
    
    
    
    29.1Asphalt
    
    
    5,289
    
    
    
    8.9
    
    
    
    4,850
    
    
    
    13.1
    
    
    
    7,620
    
    
    
    11.3Petrochemicals
    
    
    2,928
    
    
    
    4.9
    
    
    
    1,221
    
    
    
    3.3
    
    
    
    3,980
    
    
    
    5.9Other
    
    
    5,327
    
    
    
    9.0
    
    
    
    6,298
    
    
    
    17.0
    
    
    
    4,190
    
    
    
    6.2Total refinery production (9)
    
    
    59,506
    
    
    
    100.0
    
    
    
    37,074
    
    
    
    100.0
    
    
    
    67,601
    
    
    
    100.0Refinery utilization (10)
    
    
    
    
    
    
    82.3
    %
    
    
    
    
    
    
    52.3
    %
    
    
    
    
    
    
    92.5
    %
 Year Ended December 31,THROUGHPUT AND PRODUCTION DATA:
    
    2009
    
    2008
    
    2007California refineries
    
    bpd
    
    %
    
    bpd
    
    %
    
    bpd
    
    %Refinery throughput:Medium sour crude
    
    
    13,408
    
    
    
    43.0
    
    
    
    8,014
    
    
    
    25.8
    
    
    
    20,839
    
    
    
    33.7Heavy crude
    
    
    17,420
    
    
    
    55.9
    
    
    
    22,590
    
    
    
    72.6
    
    
    
    40,700
    
    
    
    65.9Blendstocks
    
    
    330
    
    
    
    1.1
    
    
    
    495
    
    
    
    1.6
    
    
    
    223
    
    
    
    0.4Total refinery throughput (8)
    
    
    31,158
    
    
    
    100.0
    
    
    
    31,099
    
    
    
    100.0
    
    
    
    61,762
    
    
    
    100.0Refinery production:Gasoline
    
    
    4,920
    
    
    
    16.2
    
    
    
    4,141
    
    
    
    13.7
    
    
    
    7,318
    
    
    
    12.1Diesel/jet
    
    
    7,123
    
    
    
    23.5
    
    
    
    7,481
    
    
    
    24.8
    
    
    
    13,360
    
    
    
    22.1Asphalt
    
    
    8,976
    
    
    
    29.5
    
    
    
    9,214
    
    
    
    30.5
    
    
    
    19,006
    
    
    
    31.5Light unfinished
    
    
    117
    
    
    
    0.4
    
    
    
    
    
    
    
    
    
    
    
    3,071
    
    
    
    5.1Heavy unfinished
    
    
    8,813
    
    
    
    29.0
    
    
    
    9,182
    
    
    
    30.4
    
    
    
    16,793
    
    
    
    27.9Other
    
    
    418
    
    
    
    1.4
    
    
    
    192
    
    
    
    0.6
    
    
    
    793
    
    
    
    1.3Total refinery production (9)
    
    
    30,367
    
    
    
    100.0
    
    
    
    30,210
    
    
    
    100.0
    
    
    
    60,341
    
    
    
    100.0Refinery utilization (10)
    
    
    
    
    
    
    46.2
    %
    
    
    
    
    
    
    46.3
    %
    
    
    
    
    
    
    85.9
    %Year Ended December 31,THROUGHPUT AND PRODUCTION DATA:
    
    2009
    
    2008Krotz Springs refinery (B)
    
    bpd
    
    %
    
    bpd
    
    %Refinery throughput:Light sweet crude
    
    
    22,942
    
    
    
    47.5
    
    
    
    43,361
    
    
    
    74.5Heavy sweet crude
    
    
    22,258
    
    
    
    46.0
    
    
    
    11,979
    
    
    
    20.6Blendstocks
    
    
    3,137
    
    
    
    6.5
    
    
    
    2,844
    
    
    
    4.9Total refinery throughput (8)
    
    
    48,337
    
    
    
    100.0
    
    
    
    58,184
    
    
    
    100.0Refinery production:Gasoline
    
    
    22,264
    
    
    
    45.4
    
    
    
    25,195
    
    
    
    42.8Diesel/jet
    
    
    21,318
    
    
    
    43.4
    
    
    
    26,982
    
    
    
    45.9Heavy oils
    
    
    1,238
    
    
    
    2.5
    
    
    
    1,402
    
    
    
    2.4Other
    
    
    4,258
    
    
    
    8.7
    
    
    
    5,258
    
    
    
    8.9Total refinery production (9)
    
    
    49,078
    
    
    
    100.0
    
    
    
    58,837
    
    
    
    100.0Refinery utilization (10)
    
    
    
    
    
    
    65.3
    %
    
    
    
    
    
    
    66.6
    %
 
 (B)
    
    The year ended December 31, 2008, represents throughput and production data for the period
from July 1, 2008 through December 31, 2008. 54




---



##### Table of Contents



(1)
    
    Net sales include inter-segment sales to our asphalt and retail and branded marketing
segments at prices which are intended to approximate wholesale market prices. These
inter-segment sales are eliminated through consolidation of our financial statements.(2)
    
    Includes $51.1 million of expenses incurred from pipeline commitment deficiencies, crude sale
losses and other incremental costs; $5.0 million for our third party liability insurance
deductible under the insurance policy; and depreciation for the temporarily idled facilities
of $0.8 million for the year ended December 31, 2008.(3)
    
    Business interruption recovery of $55.0 million was recorded for the year ended December 31,
2008 as a result of the Big Spring refinery fire with all insurance proceeds being received in
2008 and January 2009.(4)
    
    A gain on involuntary conversion of assets of $279.7 million has been recorded for the
insurance proceeds received in excess of the book value of the assets impaired of $25.3
million and demolition and repair expenses of $25.0 million incurred through December 31, 2008
as a result of the Big Spring refinery fire.(5)
    
    Gain on disposition of assets reported in 2008 primarily includes the recognition of deferred
gain recorded in connection with the HEP transaction. A recognized gain of $42.9 million
represented all the remaining deferred gain associated with the HEP transaction and was due to
the termination of an indemnification agreement with HEP. Gain on disposition of assets
reported in 2007 reflects the recognition of $7.1 million deferred gain recorded primarily in
connection with the HEP transaction.(6)
    
    Refinery operating margin is a per barrel measurement calculated by dividing the margin
between net sales and cost of sales (exclusive of unrealized hedging gains and losses and
inventories adjustments related to acquisitions) attributable to each refinery by the
refinerys throughput volumes. Industry-wide refining results are driven and measured by the
margins between refined product prices and the prices for crude oil, which are referred to as
crack spreads. We compare our refinery operating margins to these crack spreads to assess our
operating performance relative to other participants in our industry. There were unrealized
hedging gains of $0.4 million and $4.2 million for the years ended December 31, 2009 and 2008,
respectively, and an unrealized hedging loss of $4.3 million for the California refineries for
the year ended December 31, 2007. There were unrealized hedging gains of $25.6 million for the
year ended December 31, 2009 and unrealized hedging gains of $117.5 million for the Krotz
Springs refinery for the six months ended December 31, 2008. The 2008 refinery operating
margin for the Krotz Springs refinery excludes a charge of $127.4 million to cost of sales for
inventories adjustments related to the acquisition. Additionally, the Krotz Springs refinery
margin for 2009 excludes realized gains related to the unwind of the heating oil crack spread
hedge of $139.3 million.(7)
    
    Refinery direct operating expense is a per barrel measurement calculated by dividing direct
operating expenses at our Big Spring, California, and Krotz Springs refineries, exclusive of
depreciation and amortization, by the applicable refinerys total throughput volumes.(8)
    
    Total refinery throughput represents the total barrels per day of crude oil and blendstock
inputs in the refinery production process.(9)
    
    Total refinery production represents the barrels per day of various products produced from
processing crude and other refinery feedstocks through the crude units and other conversion
units at the refineries. Light product yields decreased at the Big Spring refinery for the
year ended December 31, 2008 due to the fire on February 18, 2008 and the re-start of the
crude unit in a hydroskimming mode on April 5, 2008.(10)
    
    Refinery utilization represents average daily crude oil throughput divided by crude oil
throughput capacity, excluding planned periods of downtime for maintenance and turnarounds.
The decrease in refinery utilization at our Big Spring refinery for 2008 is due to the fire on
February 18, 2008. Production ceased at the Big Spring refinery until the re-start of the
crude unit in a hydroskimming mode on April 5, 2008. The Big Spring refinery returned to a
normal operating mode with the re-start of the Fluid Catalytic Cracking Unit (FCCU) on
September 26, 2008. The decrease in refinery utilization at our California refineries is due
to reduced throughput to optimize our refining and asphalt economics. The low refinery
utilization at our Krotz Springs refinery is due to shutdowns during hurricanes Gustav and Ike
and limited crude supply and electrical outages following the hurricanes. 55




---



##### Table of Contents



ASPHALT SEGMENT
 Year Ended December 31,2009
    
    
    2008
    
    
    2007(dollars in thousands, except per ton data)STATEMENT OF OPERATIONS DATA:Net sales
    
    $
    440,915
    
    
    $
    647,221
    
    
    $
    642,937Operating costs and expenses:Cost of sales (1)
    
    
    386,050
    
    
    
    499,992
    
    
    
    592,709Direct operating expenses
    
    
    44,124
    
    
    
    43,356
    
    
    
    46,929Selling, general and administrative expenses
    
    
    4,588
    
    
    
    4,292
    
    
    
    2,825Depreciation and amortization
    
    
    6,807
    
    
    
    2,139
    
    
    
    2,145Total operating costs and expenses
    
    
    441,569
    
    
    
    549,779
    
    
    
    644,608Operating income (loss)
    
    $
    (654
    )
    
    $
    97,442
    
    
    $
    (1,671
    )KEY OPERATING STATISTICS AND OTHER DATA:Number of terminals (end of period)
    
    
    12
    
    
    
    12
    
    
    
    12Blended asphalt sales volume (tons in thousands) (2)
    
    
    994
    
    
    
    1,210
    
    
    
    1,794Non-blended asphalt sales volume (tons in thousands) (3)
    
    
    197
    
    
    
    88
    
    
    
    133Blended asphalt sales price per ton (2)
    
    $
    409.88
    
    
    $
    511.95
    
    
    $
    344.81Non-blended asphalt sales price per ton (3)
    
    
    170.05
    
    
    
    315.48
    
    
    
    183.08Asphalt margin per ton (4)
    
    
    46.07
    
    
    
    113.43
    
    
    
    26.07Capital expenditures
    
    $
    2,579
    
    
    $
    644
    
    
    $
    2,167
 
 (1)
    
    Cost of sales includes intersegment purchases of asphalt blends from our refining and
unbranded marketing segment at prices which approximate wholesale market prices. These
intersegment purchases are eliminated through consolidation of our financial statements.(2)
    
    Blended asphalt represents base asphalt that has been blended with other materials necessary
to sell the asphalt as a finished product.(3)
    
    Non-blended asphalt represents base material asphalt and other components that require
additional blending before being sold as a finished product.(4)
    
    Asphalt margin is a per ton measurement calculated by dividing the margin between net sales
and cost of sales by the total sales volume. Asphalt margins are used in the asphalt industry
to measure operating results related to asphalt sales. 56




---



##### Table of Contents



RETAIL AND BRANDED MARKETING SEGMENT (A)
 Year Ended December 31,2009
    
    
    2008
    
    
    2007(dollars in thousands, except per gallon data)STATEMENT OF OPERATIONS DATA:Net sales (1)
    
    $
    808,221
    
    
    $
    1,227,319
    
    
    $
    1,274,516Operating costs and expenses:Cost of sales (2)
    
    
    691,651
    
    
    
    1,117,712
    
    
    
    1,158,260Selling, general and administrative expenses
    
    
    94,725
    
    
    
    97,172
    
    
    
    81,933Depreciation and amortization
    
    
    13,464
    
    
    
    13,674
    
    
    
    10,245Total operating costs and expenses
    
    
    799,840
    
    
    
    1,228,558
    
    
    
    1,250,438Gain (loss) on disposition of assets
    
    
    (549
    )
    
    
    
    
    
    
    68Operating income (loss)
    
    $
    7,832
    
    
    $
    (1,239
    )
    
    $
    24,146KEY OPERATING STATISTICS AND OTHER DATA:Integrated branded fuel sales (thousands of gallons) (3)
    
    
    260,629
    
    
    
    225,474
    
    
    
    254,044Integrated branded fuel margin (cents per gallon) (3)
    
    
    5.9
    ¢
    
    
    4.4
    ¢

    
    
    9.2
    ¢Non-Integrated branded fuel sales (thousands of gallons) (3)
    
    
    13,472
    
    
    
    113,626
    
    
    
    204,537Non-Integrated branded fuel margin (cents per gallon) (3)
    
    
    3.3
    ¢

    
    
    (0.3)
    ¢

    
    
    1.3
    ¢Number of stores (end of period)
    
    
    308
    
    
    
    306
    
    
    
    307Retail fuel sales (thousands of gallons)
    
    
    120,697
    
    
    
    96,974
    
    
    
    91,946Retail fuel sales (thousands of gallons per site per month) (4)
    
    
    33
    
    
    
    27
    
    
    
    30Retail fuel margin (cents per gallon) (5)
    
    
    13.9
    ¢

    
    
    19.7
    ¢

    
    
    21.2
    ¢Retail fuel sales price (dollar per gallon) (6)
    
    $
    2.29
    
    
    $
    3.26
    
    
    $
    2.82Merchandise sales
    
    $
    268,785
    
    
    $
    261,144
    
    
    $
    220,807Merchandise sales (per site per month) (4)
    
    
    73
    
    
    
    72
    
    
    
    72Merchandise margin (7)
    
    
    30.7
    %
    
    
    30.9
    %
    
    
    32.0
    %Capital expenditures
    
    $
    3,822
    
    
    $
    2,928
    
    
    $
    9,797
 
 (A)
    
    In the first quarter of 2008, our branded marketing business was removed from the refining
and marketing segment and combined with the retail segment. Information for 2007 has been
recast to provide a comparison to the 2009 and 2008 results.(1)
    
    Includes excise taxes on sales by the retail and branded marketing segment of $47.1 million,
$37.5 million, and $35.8 million for the years ended December 31, 2009, 2008 and 2007,
respectively. Net sales also includes royalty and related net credit card fees of $0.9
million and $0.3 million for the years ended December 31, 2009 and 2008, respectively.(2)
    
    Cost of sales includes inter-segment purchases of motor fuels from our refining and unbranded
marketing segment at prices which approximate market prices. These inter-segment purchases are
eliminated through consolidation of our financial statements.(3)
    
    Marketing sales volume represents branded fuel sales to our wholesale marketing customers
located in both our integrated and non-integrated regions. The branded fuels we sell in our
integrated region are primarily supplied by the Big Spring refinery, but due to the fire on
February 18, 2008 at the Big Spring refinery, more fuel was purchased from third-party
suppliers in 2008. The branded fuels we sell in the non-integrated region are obtained from
third-party suppliers. The marketing margin represents the margin between the net sales and
cost of sales attributable to our branded fuel sales volume, expressed on a cents-per-gallon
basis and includes net credit card revenue from these sales.(4)
    
    Retail fuel and merchandise sales per site for 2009 were calculated using 306 stores for
eleven months and 308 stores for one month. Retail fuel and merchandise sales per site for
2008 were calculated using 306 stores. Retail fuel and merchandise sales per site for 2007 were calculated using 206 stores for six months
and 307 stores for six months due to the acquisition of Skinnys, Inc. on June 29, 2007.(5)
    
    Retail fuel margin represents the difference between motor fuel sales revenue and the net
cost of purchased motor fuel, including transportation costs and associated motor fuel taxes,
expressed on a cents-per-gallon basis.
Motor fuel margins are frequently used in the retail industry to measure operating results
related to motor fuel sales. 57




---



##### Table of Contents



(6)
    
    Retail fuel sales price per gallon represents the average sales price for motor fuels sold
through our retail convenience stores.(7)
    
    Merchandise margin represents the difference between merchandise sales revenues and the
delivered cost of merchandise purchases, net of rebates and commissions, expressed as a
percentage of merchandise sales revenues. Merchandise margins, also referred to as in-store
margins, are commonly used in the retail industry to measure in-store, or non-fuel, operating
results. Year Ended December 31, 2009 Compared to Year Ended December 31, 2008
 Net Sales
 Consolidated.
 Refining and Unbranded Marketing Segment.
   Asphalt Segment
 Retail and Branded Marketing Segment
 58




---



##### Table of Contents



Cost of Sales
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 Direct Operating Expenses
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Selling, General and Administrative Expenses
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 59




---



##### Table of Contents



Retail and Branded Marketing Segment
 Depreciation and Amortization
  Operating Income (Loss)
 Consolidated
 Refining and Unbranded Marketing Segment
  Asphalt Segment
 Retail and Branded Marketing Segment
 Interest Expense
  60




---



##### Table of Contents



Income Tax Expense (Benefit)
  Non-controlling Interest in Income (Loss) of Subsidiaries
  Accumulated Dividends on Preferred Stock of Subsidiary
  Net Income (Loss) Available to Common Stockholders
  Year Ended December 31, 2008 Compared to Year Ended December 31, 2007
 Net Sales
 Consolidated.
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 61




---



##### Table of Contents



Retail and Branded Marketing Segment
 Cost of Sales
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 Direct Operating Expenses
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 62




---



##### Table of Contents



Selling, General and Administrative Expenses
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 Retail and Branded Marketing Segment
 Depreciation and Amortization
  Operating Income
 Consolidated
 Refining and Unbranded Marketing Segment
 Asphalt Segment
 63




---



##### Table of Contents



Retail and Branded Marketing Segment
 Interest Expense
  Income Tax Expense
  Non-controlling Interest in Income of Subsidiaries
  Net Income Available to Common Stockholders
  Liquidity and Capital Resources
     64




---



##### Table of Contents



Cash Flow
  Year Ended December 312009
    
    
    2008
    
    
    2007(dollars in thousands)Cash provided by (used in):Operating activities
    
    $
    283,145
    
    
    $
    (812
    )
    
    $
    123,950Investing activities
    
    
    (138,691
    )
    
    
    (610,322
    )
    
    
    (147,254
    )Financing activities
    
    
    (122,471
    )
    
    
    560,973
    
    
    
    27,753Net increase (decrease) in cash and cash equivalents
    
    $
    21,983
    
    
    $
    (50,161
    )
    
    $
    4,449
 Cash Flows Provided By (Used in) Operating Activities
   Cash Flows Used In Investing Activities
   65




---



##### Table of Contents



Cash Flows Provided By (Used In) Financing Activities
   Cash and Cash Equivalents and Indebtedness
   Summary of Indebtedness
 As of December 31, 2009Amount Outstanding
    
    
    Total Facilities
    
    
    Total Availability (1)(dollars in thousands)Debt, including current portion:Term loan credit facilities
    
    $
    434,250
    
    
    $
    434,250
    
    
    $
    Revolving credit facilities
    
    
    216,577
    
    
    
    790,000
    
    
    
    149,445Senior secured notes
    
    
    205,693
    
    
    
    205,693
    
    
    
    Retail credit facilities
    
    
    80,504
    
    
    
    80,504
    
    
    
    Totals
    
    $
    937,024
    
    
    $
    1,510,447
    
    
    $
    149,445
 
 (1)
    
    Total availability was calculated as the lesser of (a) the total size of the facilities less
outstanding borrowings and letters of credit as of December 31, 2009 which was $423.7 million,
or (b) total borrowing base less outstanding borrowings and letters of credit, if applicable,
as of December 31, 2009 which was $149.4 million. Credit Facilities
 Alon USA Energy, Inc. Credit Facilities
 Term Loan Credit Facility
 66




---



##### Table of Contents



Letters of Credit Facilities.
   Alon USA, LP Credit Facilities
 Revolving Credit Facility.
     Paramount Petroleum Corporation Credit Facility
 Revolving Credit Facility.
   67




---



##### Table of Contents



Alon Refining Krotz Springs, Inc. Credit Facilities
 Term Loan Credit Facility
    Senior Secured Notes.
        68




---



##### Table of Contents



Revolving Credit Facility.
         Retail Credit Facilities
    69




---



##### Table of Contents



Other Retail Related Credit Facilities
  Capital Spending
  2010
    
    
    2011(dollars in thousands)Refining and Unbranded Marketing Segment:Sustaining maintenance
    
    $
    32,791
    
    
    $
    54,595Growth/profit improvement/other
    
    
    439
    
    
    
    10,700Chemical catalyst and turnaround
    
    
    14,635
    
    
    
    22,776Total
    
    
    47,865
    
    
    
    88,071Asphalt Segment:Sustaining maintenance
    
    
    5,546
    
    
    
    4,000Growth/profit improvement
    
    
    1,425
    
    
    
    8,680Total
    
    
    6,971
    
    
    
    12,680Retail and Branded Marketing Segment:Sustaining maintenance
    
    
    7,316
    
    
    
    5,045Growth/profit improvement
    
    
    6,818
    
    
    
    3,000Total
    
    
    14,134
    
    
    
    8,045Corporate Segment:Sustaining
    
    
    2,975
    
    
    
    3,421Total Capital Expenditures
    
    $
    71,945
    
    
    $
    112,217
 Turnaround and Chemical Catalyst Costs
  2010
    
    
    2011
    
    
    2012
    
    
    2013
    
    
    2014(dollars in thousands)Scheduled turnaround costs
    
    $
    2,400
    
    
    $
    4,050
    
    
    $
    7,800
    
    
    $
    17,400
    
    
    $
    5,100Chemical catalyst costs
    
    
    12,235
    
    
    
    18,726
    
    
    
    11,343
    
    
    
    11,667
    
    
    
    24,368Total
    
    $
    14,635
    
    
    $
    22,776
    
    
    $
    19,143
    
    
    $
    29,067
    
    
    $
    29,468
 70




---



##### Table of Contents



Contractual Obligations and Commercial Commitments
  Payments Due by PeriodLess Than
    
    
    
    
    
    
    
    
    
    
    More ThanContractual Obligations
    
    1 Year
    
    
    1-3 Years
    
    
    3-5 Years
    
    
    5 Years
    
    
    Total(dollars in thousands)Long-term debt obligations
    
    $
    10,946
    
    
    $
    67,192
    
    
    $
    810,533
    
    
    $
    48,353
    
    
    $
    937,024Operating lease obligations
    
    
    35,950
    
    
    
    56,072
    
    
    
    25,707
    
    
    
    65,025
    
    
    
    182,754Pipelines and Terminals Agreement (1)
    
    
    27,549
    
    
    
    55,098
    
    
    
    55,099
    
    
    
    151,572
    
    
    
    289,318Other commitments (2)
    
    
    2,828
    
    
    
    5,655
    
    
    
    5,654
    
    
    
    20,499
    
    
    
    34,636Total obligations
    
    $
    77,273
    
    
    $
    184,017
    
    
    $
    896,993
    
    
    $
    285,449
    
    
    $
    1,443,732
 
 (1)
    
    Balances represent the minimum committed volume multiplied by the tariff and terminal rates
pursuant to the terms of the Pipelines and Terminals Agreement with HEP, as well as our
minimum requirements with Sunoco.(2)
    
    Other commitments include refinery maintenance services costs.   Off-Balance Sheet Arrangements
  Critical Accounting Policies
  Inventory
 71




---



##### Table of Contents



Environmental and Other Loss Contingencies
 Turnarounds and Chemical Catalyst Costs
 Impairment of Long-Lived Assets Accounting for the Impairment or Disposal of Long-Lived Assets
 Deferred Income Taxes
 Asset Retirement Obligations Accounting for Asset Retirement Obligations
  72




---



##### Table of Contents



Goodwill and Intangible Assets
  New Accounting Standards and Disclosures
 The FASB
Accounting Standards Codification and the Hierarchy of Generally Accepted Accounting Principles a
replacement of FASB Statement No. 162
 Subsequent Events
 Employers Disclosures
about Postretirement Benefit Plans Employers Disclosures about Pensions and Other
Postretirement Benefits
 Equity Method
Investment Accounting Considerations
 73




---



##### Table of Contents



Accounting by Lessees
for Maintenance Deposits
 Determination of the Useful Life
of Intangible Assets Goodwill and Other Intangible Assets.
 Disclosure about Derivative Instruments and
Hedging Activities
 Fair Value
Measurements
 Partial Deferral of the
Effective Date of Statement 157
 The Fair Value Option for Financial Assets and
Financial Liabilities
 Non-controlling Interests in Consolidated
Financial Statements, an Amendment of ARB 51
 74




---



##### Table of Contents



December 31,
    
    
    
    
    
    
    December 31,2008
    
    
    Adjustments
    
    
    2008(aspreviouslyreported)
    
    
    
    
    
    
    (recast)Total stockholders equity
    
    $
    431,919
    
    
    $
    2,732
    
    
    $
    434,651Non-controlling interest in subsidiaries (1)
    
    
    
    
    
    
    17,916
    
    
    
    17,916Preferred stock of subsidiary including accumulated dividends (1)
    
    
    
    
    
    
    84,300
    
    
    
    84,300Total equity
    
    $
    431,919
    
    
    $
    104,948
    
    
    $
    536,867
 
 (1)
    
    Previously reported outside of equity.  Business Combinations
 Reconciliation of Amounts Reported Under Generally Accepted Accounting Principles
 Reconciliation of Adjusted EBITDA to amounts reported under generally accepted accounting
principles in financial statements.
   
    
    Adjusted EBITDA does not reflect our cash expenditures or future requirements for
capital expenditures or contractual commitments;
    
    Adjusted EBITDA does not reflect the interest expense or the cash requirements
necessary to service interest or principal payments on our debt;
    
    Adjusted EBITDA does not reflect the prior claim that non-controlling interest have
on the income generated by non-wholly-owned subsidiaries;
    
    Adjusted EBITDA does not reflect changes in or cash requirements for our working
capital needs; and
 75




---



##### Table of Contents




    
    Our calculation of Adjusted EBITDA may differ from EBITDA calculations of other
companies in our industry, limiting its usefulness as a comparative measure.
   For the Year Ended December 31,2009
    
    
    2008
    
    
    2007(in thousands)Net income (loss)
    
    $
    (115,156
    )
    
    $
    82,883
    
    
    $
    103,936Non-controlling interest in income
(loss) of subsidiaries (including
accumulated dividends on preferred
stock of subsidiary)
    
    
    12,949
    
    
    
    10,241
    
    
    
    5,979Income tax expense (benefit)
    
    
    (64,877
    )
    
    
    62,781
    
    
    
    46,199Interest expense
    
    
    111,137
    
    
    
    67,550
    
    
    
    47,747Depreciation and amortization
    
    
    97,247
    
    
    
    66,754
    
    
    
    57,403(Gain) loss on disposition of assets
    
    
    1,591
    
    
    
    (45,244
    )
    
    
    (7,206
    )Adjusted EBITDA
    
    $
    42,891
    
    
    $
    244,965
    
    
    $
    254,058
  
 ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK.
 Quantitative and Qualitative Disclosure About Market Risk
  Commodity Price Risk
    76




---



##### Table of Contents



Contract
    
    Wtd AvgVolume
    
    Purchase
    
    Wtd Avg
    
    ContractDescription of Activity
    
    (in barrels)
    
    Price
    
    Sales Price
    
    Value
    
    Fair Value
    
    Gain (Loss)Futures-long (Crude)
    
    
    240,000
    
    
    $
    71.95
    
    
    $
    
    
    
    $
    17,268
    
    
    $
    19,046
    
    
    $
    1,778Futures-short (Crude)
    
    
    (240,000
    )
    
    
    
    
    
    
    80.63
    
    
    
    (17,895
    )
    
    
    (19,351
    )
    
    
    (1,456
    )
 ContractVolume
    
    Wtd Avg
    
    Wtd Avg
    
    ContractDescription of Activity
    
    (in barrels)
    
    Contract
    
    Sales Price
    
    Value
    
    Fair Value
    
    Gain (Loss)Futures-crack spread (Heating Oil)
    
    
    364,800
    
    
    $
    11.38
    
    
    $
    11.62
    
    
    $
    4,150
    
    
    $
    4,239
    
    
    $
    89Futures-long (SPR swaps)
    
    
    278,322
    
    
    
    95.92
    
    
    
    81.59
    
    
    
    26,696
    
    
    
    22,708
    
    
    
    (3,988
    )Futures-short (SPR swaps)
    
    
    (278,322
    )
    
    
    60.05
    
    
    
    81.59
    
    
    
    (16,713
    )
    
    
    (22,708
    )
    
    
    (5,995
    )
 Interest Rate Risk
   
 ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA.
  
 ITEM 9. CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING AND FINANCIAL DISCLOSURE.
  
 ITEM 9A. CONTROLS AND PROCEDURES.
 Disclosure Controls and Procedures
  77




---



##### Table of Contents



Managements Report on Internal Control over Financial Reporting
  Changes in Internal Control Over Financial Reporting
  Certifications
  
 ITEM 9B. OTHER INFORMATION.
  78




---



##### Table of Contents



PART III
 
 ITEM 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE.
    
 ITEM 11. EXECUTIVE COMPENSATION.
  
 ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER
MATTERS.
  
 ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS, AND DIRECTOR INDEPENDENCE.
  
 ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES.
  79




---



##### Table of Contents



PART IV
 
 ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES.
 (a)
    
    The following documents are filed as part of this report:(1)
    
    Consolidated Financial Statements and Schedule, see Index to Consolidated Financial
Statements and Schedule on page F-1.(a)
    
    Schedule II  Valuation and Qualifying accounts is included in the Notes to Consolidated
Financial Statements.(2)
    
    Exhibits: Reference is made to the Index of Exhibits immediately preceding the exhibits
hereto, which index is incorporated herein by reference.
 Exhibit No.
    
    Description of Exhibit3.1
    
    Amended and Restated Certificate of Incorporation of Alon USA Energy, Inc. (incorporated by
reference to Exhibit 3.1 to Form S-1/A, filed by the Company on July 7, 2005, SEC File No.
333-124797).3.2
    
    Amended and Restated Bylaws of Alon USA Energy, Inc. (incorporated by reference to Exhibit
3.2 to Form S-1/A, filed by the Company on July 14, 2005, SEC File No. 333-124797).4.1
    
    Specimen Common Stock Certificate (incorporated by reference to Exhibit 4.1 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).4.2
    
    Indenture, dated as of October 22, 2009, by and among Alon Refining Krotz Springs, Inc. and
Wilmington Trust FSB, as Trustee (incorporated by reference to Exhibit 4.1 to Form 8-K,
filed by the Company on October 23, 2009, SEC File No. 001-32567).10.1
    
    Trademark License Agreement, dated as of July 31, 2000, among Finamark, Inc., Atofina
Petrochemicals, Inc. and SWBU, L.P. (incorporated by reference to Exhibit 10.3 to Form S-1,
filed by the Company on May 11, 2005, SEC File No. 333-124797).10.2
    
    First Amendment to Trademark License Agreement, dated as of April 11, 2001, among Finamark,
Inc., Atofina Petrochemicals, Inc. and SWBU, L.P. (incorporated by reference to Exhibit 10.4
to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.3
    
    Pipeline Lease Agreement, dated as of December 12, 2007, between Plains Pipeline, L.P. and
Alon USA, L.P. (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company
on February 2, 2008, SEC File No. 001-32567).10.4
    
    Pipeline Lease Agreement, dated as of February 21, 1997, between Navajo Pipeline Company and
American Petrofina Pipe Line Company (incorporated by reference to Exhibit 10.6 to Form S-1,
filed by the Company on May 11, 2005, SEC File No. 333-124797).10.5
    
    Amendment and Supplement to Pipeline Lease Agreement, dated as of August 31, 2007, by and
between HEP Pipeline Assets, Limited Partnership and Alon USA, LP (incorporated by reference
to Exhibit 10.1 to Form 10-Q, filed by the Company on November 8, 2007).10.6
    
    Contribution Agreement, dated as of January 25, 2005, among Holly Energy Partners, L.P.,
Holly Energy Partners  Operating, L.P., T & R Assets, Inc., Fin-Tex Pipe Line Company,
Alon USA Refining, Inc., Alon Pipeline Assets, LLC, Alon Pipeline Logistics, LLC, Alon USA,
Inc. and Alon USA, LP (incorporated by reference to Exhibit 10.7 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.7
    
    Pipelines and Terminals Agreement, dated as of February 28, 2005, between Alon USA, LP and
Holly Energy Partners, L.P. (incorporated by reference to Exhibit 10.8 to Form S-1, filed by
the Company on May 11, 2005, SEC File No. 333-124797).10.8
    
    Pipeline Lease Agreement, dated as of December 12, 2007, between Plains Pipeline, L.P. and
Alon USA, LP (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on
February 5, 2008, SEC File No. 001-32567).
 80




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.9
    
    Liquor License Purchase Agreement, dated as of May 12, 2003, between Southwest Convenience
Stores, LLC and SCS Beverage, Inc. (incorporated by reference to Exhibit 10.34 to Form
S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.10
    
    Premises Lease, dated as of May 12, 2003, between Southwest Convenience Stores, LLC and SCS
Beverage, Inc. (incorporated by reference to Exhibit 10.35 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.11
    
    Registration Rights Agreement, dated as of July 6, 2005, between Alon USA Energy, Inc. and
Alon Israel Oil Company, Ltd. (incorporated by reference to Exhibit 10.22 to Form S-1/A,
filed by the Company on July 7, 2005, SEC File No. 333-124797).10.12
    
    Registration Rights Agreement, dated October 22, 2009, between Alon Refining Krotz Springs,
Inc. and Jefferies & Company, Inc. (incorporated by reference to Exhibit 10.2 to Form 8-K,
filed by the Company on October 23, 2009, SEC File No. 001-32567).10.13
    
    Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA, LP, EOC
Acquisition, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.2 to Form 8-K, filed by the Company on June 26, 2006, SEC File
No. 001-32567).10.14
    
    First Amendment to Amended Revolving Credit Agreement, dated as of August 4, 2006, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA, LP, EOC
Acquisition, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.25 to Form 10-K, filed by the Company on March 15, 2007 SEC File
No. 001-32567).10.15
    
    Waiver, Consent, Partial Release and Second Amendment, dated as of February 28, 2007, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, Alon USA, LP, Edgington Oil
Company, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other guarantor
companies and financial institutions from time to time named therein (incorporated by
reference to Exhibit 10.2 to Form 8-K, filed by the Company on March 5, 2007, SEC File No.
001-32567).10.16
    
    Third Amendment to Amended Revolving Credit Agreement, dated as of June 29, 2007, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA Energy, Inc.,
Alon USA, LP, the guarantor companies and financial institutions named therein, Israel
Discount Bank of New York and Bank Leumi USA (incorporated by reference to Exhibit 10.1 to
Form 8-K, filed by the Company on July 20, 2007, SEC File No. 001-32567).10.17
    
    Waiver, Consent, Partial Release and Fourth Amendment, dated as of July 2, 2008, by and
among Alon USA, LP, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.4 to Form 8-K, filed by the Company on July 10, 2008, SEC File
No. 001-32567).10.18
    
    Fifth Amendment to Amended Revolving Credit Agreement, dated as of July 31, 2009, by and
among Alon USA, LP, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.3 to Form 10-Q, filed by the Company on August 6, 2009, SEC File
No. 001-32567).10.19
    
    Credit Agreement, dated as of July 30, 2008, among Alon USA Energy, Inc., the financial
institutions from time to time party thereto, Israel Discount Bank and Bank Leumi USA
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on August 1,
2008, SEC File No. 001-32567).10.20
    
    Amended and Restated Credit Agreement, dated as of June 29, 2007, among Southwest
Convenience Stores, LLC, the lenders party thereto and Wachovia Bank, National Association
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on July 2,
2007, SEC File No. 001-32567).10.21
    
    Credit Agreement, dated as of June 22, 2006, among Alon USA Energy, Inc., the lenders party
thereto and Credit Suisse (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by
the Company on June 26, 2006, SEC File No. 001-32567).
 81




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.22
    
    Amendment No. 1 to the Credit Agreement, dated as of February 28, 2007, by and among Alon
USA Energy, Inc., the lenders party thereto and Credit Suisse (incorporated by reference to
Exhibit 10.3 to Form 8-K, filed by the Company on March 5, 2007, SEC File No. 001-32567).10.23
    
    Second Amended and Restated Credit Agreement, dated as of February 28, 2007, among Paramount
Petroleum Corporation, Bank of America, N.A. and certain other guarantor companies and
financial institutions from time to time named therein (incorporated by reference to Exhibit
10.1 to Form 8-K, filed by the Company on March 5, 2007, SEC File No. 001-32567).10.24
    
    First Amendment to Second Amended and Restated Credit Agreement, dated as of March 30, 2007,
among Paramount Petroleum Corporation, Bank of America, N.A. and certain other guarantor
companies and financial institutions from time to time named therein (incorporated by
reference to Exhibit 10.37 to Form 10-K, filed by the Company on March 11, 2008, SEC File
No. 001-32567).10.25
    
    Term Loan Agreement, dated as of July 3, 2008, by and among Alon Refining Louisiana, Inc.,
Alon Refining Krotz Springs, Inc., the lenders party thereto and Credit Suisse, as
administrative agent and collateral agent (incorporated by reference to Exhibit 10.2 to Form
8-K, filed by the Company on July 10, 2008, SEC File No. 001-32567).10.26
    
    First Amendment Agreement, dated as of April 9, 2009, by and among Alon Refining Louisiana,
Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto and Wells Fargo Bank, National
Association, as successor to Credit Suisse, Cayman Islands Branch, as agent (incorporated by
reference to Exhibit 10.1 to Form 10-Q, filed by the Company on August 6, 2009, SEC File No.
001-32567).10.27
    
    Loan and Security Agreement, dated as of July 3, 2008, by and among Alon Refining Louisiana,
Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto and Bank of America,
N.A., as administrative agent (incorporated by reference to Exhibit 10.3 to Form 8-K, filed
by the Company on July 10, 2008, SEC File No. 001-32567).10.28
    
    First Amendment to Loan and Security Agreement, dated as of December 18, 2008, by and among
Alon Refining Louisiana, Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto
and Bank of America, N.A. (incorporated by reference to Exhibit 10.28 to Form 10-K, filed by
the Company on April 10, 2009, SEC File No. 001-32567).10.29
    
    Second Amendment to Loan and Security Agreement, dated as of April 9, 2009, by and among
Alon Refining Louisiana, Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto and Bank
of America, N.A., as agent (incorporated by reference to Exhibit 10.2 to Form 8-K, filed by
the Company on April 27, 2009, SEC File No. 001-32567).10.30
    
    Amended and Restated Loan and Security Agreement, dated as of October 22, 2009 (as amended,
supplemented or otherwise modified from time to time), among Alon Refining Louisiana, Inc.,
Alon Refining Krotz Springs, Inc., each other party joined as a borrower thereunder from
time to time, the Lenders party thereto, and Bank of America, N.A., as Agent (incorporated
by reference to Exhibit 10.1 to Form 8-K, filed by the Company on October 23, 2009, SEC File
No. 001-32567).10.31
    
    Purchase Agreement dated October 13, 2009, between Alon Refining Krotz Springs, Inc. and
Jefferies & Co. (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company
on October 19, 2009, SEC File No. 001-32567).10.32
    
    Management and Consulting Agreement, dated as of August 1, 2003, among Alon USA, Inc., Alon
Israel Oil Company, Ltd. and Alon USA Energy, Inc. (incorporated by reference to Exhibit
10.21 to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.33
    
    Amendment, dated as of June 17, 2005, to the Management and Consulting Agreement, dated as
of August 1, 2003, among Alon USA, Inc., Alon Israel Oil Company, Ltd. and Alon USA Energy,
Inc. (incorporated by reference to Exhibit 10.21.1 to Form S-1/A, filed by the Company on
June 17, 2005, SEC File No. 333-124797).10.34*
    
    Executive Employment Agreement, dated as of July 31, 2000, between Jeff D. Morris and Alon
USA GP, Inc., as amended by the Amendment to Executive/Management Employment Agreement,
dated May 1, 2005 (incorporated by reference to Exhibit 10.23 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).
 82




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.35*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon USA GP, LLC (incorporated by reference to Exhibit 10.9 to Form 10-Q,
filed by the Company on November 7, 2008, SEC File No. 001-32567).10.36*
    
    Executive Employment Agreement, dated as of July 31, 2000, between Claire A. Hart and Alon
USA GP, Inc., as amended by the Amendment to Executive/Management Employment Agreement,
dated May 1, 2005 (incorporated by reference to Exhibit 10.24 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.37*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Claire A. Hart and Alon USA GP, LLC (incorporated by reference to Exhibit 10.10 to Form
10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.38*
    
    Executive Employment Agreement, dated as of February 5, 2001, between Joseph A. Concienne,
III and Alon USA GP, Inc., as amended by the Amendment to Executive/Management Employment
Agreement, dated May 1, 2005 (incorporated by reference to Exhibit 10.25 to Form S-1, filed
by the Company on May 11, 2005, SEC File No. 333-124797).10.39*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Joseph A. Concienne, III and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.11
to Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.40*
    
    Amended and Restated Management Employment Agreement, dated as of August 9, 2006, between
Harlin R. Dean and Alon USA GP, LLC (incorporated by reference to Exhibit 10.1 to Form 8-K,
filed by the Company on August 10, 2006, SEC File No. 001-32567).10.41*
    
    Amendment to Amended and Restated Management Employment Agreement, dated as of November 4,
2008, between Harlin R. Dean and Alon USA GP, LLC (incorporated by reference to Exhibit
10.12 to Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.42*
    
    Management Employment Agreement, dated as of September 1, 2000, between Yosef Israel and
Alon USA GP, LLC (incorporated by reference to Exhibit 10.33 to Form 10-K, filed by the
Company on March 15, 2006, SEC File No. 001-32567).10.43*
    
    Amendment to Executive/Management Employment Agreement, dated as of May 1, 2005 between
Yosef Israel and Alon USA GP, LLC (incorporated by reference to Exhibit 10.34 to Form 10-K,
filed by the Company on March 15, 2006, SEC File No. 001-32567).10.44*
    
    Second Amendment to Executive/Management Employment Agreement, dated as of November 4, 2008,
between Yosef Israel and Alon USA GP, LLC (incorporated by reference to Exhibit 10.13 to
Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.45*
    
    Executive Employment Agreement, dated as of August 1, 2003, between Shai Even and Alon USA
GP, LLC (incorporated by reference to Exhibit 10.49 to Form 10-K, filed by the Company on
March 15, 2007, SEC File No. 001-32567).10.46*
    
    Amendment to Executive Employment Agreement, dated as of November 4, 2008, between Shai Even
and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.14 to Form 10-Q, filed by the
Company on November 7, 2008, SEC File No. 001-32567).10.47*
    
    Agreement of Principles of Employment, dated as of July 6, 2005, between David Wiessman and
Alon USA Energy, Inc. (incorporated by reference to Exhibit 10.50 to Form S-1/A, filed by
the Company on July 7, 2005, SEC File No. 333-124797).10.48*
    
    Management Employment Agreement, dated as of October 30, 2008, between Michael Oster and
Alon USA GP, LLC (incorporated by reference to Exhibit 10.71 to Form 10-K, filed by the
Company on April 10, 2009, SEC File No. 001-32567).10.49*
    
    Annual Cash Bonus Plan (incorporated by reference to Exhibit 10.27 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.50*
    
    Description of 10% Bonus Plan (incorporated by reference to Exhibit 10.28 to Form S-1, filed
by the Company on May 11, 2005, SEC File No. 333-124797).10.51*
    
    Description of Annual Bonus Plans (incorporated by reference to Exhibit 10.2 to Form 10-Q,
filed by the Company on May 6, 2008, SEC File No. 001-32567).
 83




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.52*
    
    Change of Control Incentive Bonus Program (incorporated by reference to Exhibit 10.29 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.53*
    
    Description of Director Compensation (incorporated by reference to Exhibit 10.30 to Form
S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.54*
    
    Form of Director Indemnification Agreement (incorporated by reference to Exhibit 10.31 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.55*
    
    Form of Officer Indemnification Agreement (incorporated by reference to Exhibit 10.32 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.56*
    
    Form of Director and Officer Indemnification Agreement (incorporated by reference to Exhibit
10.33 to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.57*
    
    Alon Assets, Inc. 2000 Stock Option Plan (incorporated by reference to Exhibit 10.36 to Form
S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.58*
    
    Alon USA Operating, Inc. 2000 Stock Option Plan (incorporated by reference to Exhibit 10.37
to Form S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.59*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and
Jeff D. Morris, as amended by the Amendment to the Incentive Stock Option Agreement, dated
June 30, 2002 (incorporated by reference to Exhibit 10.38 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.60*
    
    Second Amendment to Incentive Stock Option Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon Assets, Inc. (incorporated by reference to Exhibit 10.15 to Form
10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.61
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and Jeff D.
Morris, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.39 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.62*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon USA Operating,
Inc. and Jeff D. Morris, as amended by the Amendment to the Incentive Stock Option
Agreement, dated June 30, 2002 (incorporated by reference to Exhibit 10.40 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.63*
    
    Second Amendment to Incentive Stock Option Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon USA Operating, Inc. (incorporated by reference to Exhibit 10.16 to
Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.64
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon USA Operating, Inc. and Jeff
D. Morris, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.41 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.65*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and
Claire A. Hart, as amended by the Amendment to the Incentive Stock Option Agreement, dated
June 30, 2002 and July 25, 2002 (incorporated by reference to Exhibit 10.42 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.66
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and Claire A.
Hart, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.43 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.67*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon USA Operating,
Inc. and Claire A. Hart, as amended by the Amendment to the Incentive Stock Option
Agreement, dated June 30, 2002 and July 25, 2002 (incorporated by reference to Exhibit 10.44
to Form S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).
 84




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.68
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon USA Operating, Inc. and
Claire A. Hart, as amended by the Amendment to the Shareholder Agreement, dated June 30,
2002 (incorporated by reference to Exhibit 10.45 to Form S-1/A, filed by the Company on June
17, 2005, SEC File No. 333-124797).10.69*
    
    Incentive Stock Option Agreement, dated as of February 5, 2001, between Alon Assets, Inc.
and Joseph A. Concienne, III, as amended by the Amendment to the Incentive Stock Option
Agreement, dated July 25, 2002 (incorporated by reference to Exhibit 10.46 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.70
    
    Shareholder Agreement, dated as of February 5, 2001, between Alon Assets, Inc. and Joseph A.
Concienne, III (incorporated by reference to Exhibit 10.47 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.71*
    
    Incentive Stock Option Agreement, dated as of February 5, 2001, between Alon USA Operating,
Inc. and Joseph A. Concienne, III, as amended by the Amendment to the Incentive Stock Option
Agreement, dated July 25, 2002 (incorporated by reference to Exhibit 10.48 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.72
    
    Shareholder Agreement, dated as of February 5, 2001, between Alon USA Operating, Inc. and
Joseph A. Concienne, III (incorporated by reference to Exhibit 10.49 to Form S-1/A, filed by
the Company on June 17, 2005, SEC File No. 333-124797).10.73
    
    Agreement, dated as of July 6, 2005, among Alon USA Energy, Inc., Alon USA, Inc., Alon USA
Capital, Inc., Alon USA Operating, Inc., Alon Assets, Inc., Jeff D. Morris, Claire A. Hart
and Joseph A. Concienne, III (incorporated by reference to Exhibit 10.52 to Form S-1/A,
filed by the Company on July 7, 2005, SEC File No. 333-124797).10.74*
    
    Alon USA Energy, Inc. 2005 Incentive Compensation Plan, as amended on November 7, 2005
(incorporated by reference to Exhibit 10.2 to Form 8-K, filed by the Company on November 8,
2005, SEC File No. 001-32567).10.75*
    
    Form of Restricted Stock Award Agreement relating to Director Grants pursuant to Section 12
of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by reference to
Exhibit 10.1 to Form 8-K, filed by the Company on August 5, 2005, SEC File No. 001-32567).10.76*
    
    Form of Restricted Stock Award Agreement relating to Participant Grants pursuant to Section
8 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by reference
to Exhibit 10.1 to Form 8-K, filed by the Company on August 23, 2005, SEC File No.
001-32567).10.77*
    
    Form II of Restricted Stock Award Agreement relating to Participant Grants pursuant to
Section 8 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.3 to Form 8-K, filed by the Company on November 8, 2005, SEC File
No. 001-32567).10.78*
    
    Form of Appreciation Rights Award Agreement relating to Participant Grants pursuant to
Section 7 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.1 to Form 8-K, filed by the Company on March 12, 2007, SEC File No.
001-32567).10.79*
    
    Form of Amendment to Appreciation Rights Award Agreement relating to Participant Grants
pursuant to Section 7 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan
(incorporated by reference to Exhibit 10.2 to Form 8-K, filed by the Company on January 27,
2010, SEC File No. 001-32567).10.80*
    
    Form II of Appreciation Rights Award Agreement relating to Participant Grants pursuant to
Section 7 of the Alon USA Energy, inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.1 to Form 8-K, filed by the Company on January 27, 2010, SEC File
No. 001-32567).10.81
    
    Purchase and Sale Agreements, dated as of February 13, 2006, between Alon Petroleum Pipe
Line, LP and Sunoco Pipelines, LP, (incorporated by reference to Exhibit 10.1 to Form 8-K,
filed by the Company on February 13, 2006, SEC File No. 001-32567).10.82
    
    Stock Purchase Agreement, dated as of April 28, 2006, among Alon USA Energy, Inc., The Craig
C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The Jerrel C. Barto and
Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy, III and Mark R. Milano
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on May 2, 2006,
SEC File No. 001-32567).
 85




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.83
    
    First Amendment to Stock Purchase Agreement, dated as of June 30, 2006, among Alon USA
Energy, Inc., The Craig C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The
Jerrel C. Barto and Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy III
and Mark R. Milano (incorporated by reference to Exhibit 10.1 to Form 10-Q, filed by the
Company on November 14, 2006, SEC File No. 001-32567).10.84
    
    Second Amendment to Stock Purchase Agreement, dated as of July 31, 2006, among Alon USA
Energy, Inc., The Craig C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The
Jerrel C. Barto and Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy III
and Mark R. Milano (incorporated by reference to Exhibit 10.2 to Form 10-Q, filed by the
Company on November 14, 2006, SEC File No. 001-32567).10.85
    
    Agreement and Plan of Merger, dated as of April 28, 2006, among Alon USA Energy, Inc., Apex
Oil Company, Inc., Edgington Oil Company, and EOC Acquisition, LLC (incorporated by
reference to Exhibit 10.2 to Form 8-K, filed by the Company on May 2, 2006, SEC File No.
001-32567).10.86
    
    Agreement and Plan of Merger, dated March 2, 2007, by and among Alon USA Energy, Inc., Alon
USA Interests, LLC, ALOSKI, LLC, Skinnys, Inc. and the Davis Shareholders (as defined
therein) (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on
March 6, 2007, SEC File No. 001-32567).10.87
    
    Stock Purchase Agreement, dated May 7, 2008, between Valero Refining and Marketing Company
and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.1 to Form
8-K, filed by the Company on May 13, 2008, SEC File No. 001-32567).10.88
    
    First Amendment to Stock Purchase Agreement, dated as of July 3, 2008, by and among Valero
Refining and Marketing Company, Alon Refining Krotz Springs, Inc. and Valero Refining
Company-Louisiana (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the
Company on July 10, 2008, SEC File No. 001-32567).10.89
    
    Series A Preferred Stock Purchase Agreement, dated as of July 3, 2008, by and between Alon
Refining Louisiana, Inc. and Alon Israel Oil Company, Ltd. (incorporated by reference to
Exhibit 10.5 to Form 8-K, filed by the Company on July 10, 2008, SEC File No. 001-32567).10.90
    
    Stockholders Agreement, dated as of July 3, 2008, by and among Alon USA Energy, Inc., Alon
Refining Louisiana, Inc., Alon Louisiana Holdings, Inc. and Alon Israel Oil Company, Ltd.
(incorporated by reference to Exhibit 10.6 to Form 8-K, filed by the Company on July 10,
2008, SEC File No. 001-32567).10.91
    
    Amended and Restated Stockholders Agreement dated as of March 31, 2009, by and among Alon
USA Energy, Inc., Alon Refining Louisiana, Inc., Alon Louisiana Holdings, Inc. and Alon
Israel Oil Company, Ltd. (incorporated by reference to Exhibit 10.88 to Form 10-K, filed by
the Company on April 10, 2009, SEC File No. 001-32567).10.92
    
    First Amendment to Amended and Restated Stockholders Agreement dated as of December 31,
2009, by and among Alon USA Energy, Inc., Alon Refining Louisiana, Inc., Alon Louisiana
Holdings, Inc. and Alon Israel Oil Company, Ltd. (incorporated by reference to Exhibit 10.1
to Form 8-K, filed by the Company on January 5, 2010, SEC File No. 001-32567).10.93
    
    Offtake Agreement, dated as of July 3, 2008, by and between Valero Marketing and Supply
Company and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.9 to
Form 10-Q, filed by the Company on August 8, 2008, SEC File No. 001-32567).10.94
    
    Earnout Agreement, dated as of July 3, 2008, by and between Valero Refining and Marketing
Company and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.10 to
Form 10-Q, filed by the Company on August 8, 2008, SEC File No. 001-32567).10.95
    
    First Amendment to Earnout Agreement, dated as of August 27, 2009, by and between Valero
Refining and Marketing Company and Alon Refining Krotz Springs, Inc. (incorporated by
reference to Exhibit 10.1 to Form 10-Q, filed by the Company on November 6, 2009, SEC File
No. 001-32567).10.96
    
    Revolving Credit Line Agreement dated March 9, 2010 by and between the Company and Israel Discount Bank of New York.10.97
    
    Credit Agreement dated as of March 15, 2010 (as amended, supplemented or otherwise
modified from time to time), among the Company, each other party joined as a
borrower thereunder from time to time, the Lenders party thereto, and Bank Hapoalim B.M., as Administrative Agent.
 86




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit12.1
    
    Statement Regarding Computation of
Ratio of Earnings to Fixed Charges.21.1
    
    Subsidiaries of Alon USA Energy, Inc.23.1
    
    Consent of KPMG LLP.31.1
    
    Certifications of Chief Executive Officer pursuant to §302 of the Sarbanes-Oxley Act of 2002.31.2
    
    Certifications of Chief Financial Officer pursuant to §302 of the Sarbanes-Oxley Act of 2002.32.1
    
    Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C.
§1350, as adopted pursuant to §906 of the Sarbanes-Oxley Act of 2002.
 
 *
    
    Identifies management contracts and compensatory plans or arrangements.
    
    Filed under confidential treatment request. 87




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
 INDEX TO CONSOLIDATED FINANCIAL STATEMENTS AND SCHEDULE
 PageAudited Consolidated Financial Statements:Report of Independent Registered Public Accounting Firm
    
    
    F-2Consolidated Balance Sheets as of December 31, 2009 and 2008
    
    
    F-4Consolidated Statements of Operations for the Years Ended December 31, 2009, 2008 and 2007
    
    
    F-5Consolidated Statements of Stockholders Equity for the Years Ended December 31, 2009, 2008 and 2007
    
    
    F-6Consolidated Statements of Cash Flows for the Years Ended December 31, 2009, 2008 and 2007
    
    
    F-7Notes to Consolidated Financial Statements
    
    
    F-9
 F-1




---



##### Table of Contents



REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
 
     Internal Control Integrated Framework
  
 F-2




---



##### Table of Contents



REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
 
 Internal ControlIntegrated Framework Managements Report on Internal Control over Financial Reporting
    Internal ControlIntegrated Framework
   
 F-3




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
CONSOLIDATED BALANCE SHEETS
(in thousands except share data)
 As of December 31,2009
    
    
    2008ASSETSCurrent assets:Cash and cash equivalents
    
    $
    40,437
    
    
    $
    18,454Accounts and other receivables, net
    
    
    103,094
    
    
    
    204,576Income tax receivable
    
    
    65,418
    
    
    
    116,564Inventories
    
    
    214,999
    
    
    
    232,320Deferred income tax asset
    
    
    7,700
    
    
    
    Prepaid expenses and other current assets
    
    
    4,188
    
    
    
    81,758Total current assets
    
    
    435,836
    
    
    
    653,672Equity method investments
    
    
    43,052
    
    
    
    37,661Property, plant, and equipment, net
    
    
    1,477,426
    
    
    
    1,448,959Goodwill
    
    
    105,943
    
    
    
    105,943Other assets
    
    
    70,532
    
    
    
    167,198Total assets
    
    $
    2,132,789
    
    
    $
    2,413,433LIABILITIES AND STOCKHOLDERS EQUITYCurrent liabilities:Accounts payable
    
    $
    248,253
    
    
    $
    233,004Accrued liabilities
    
    
    92,380
    
    
    
    111,317Current portion of long-term debt
    
    
    10,946
    
    
    
    28,397Deferred income tax liability
    
    
    
    
    
    
    30,570Total current liabilities
    
    
    351,579
    
    
    
    403,288Other non-current liabilities
    
    
    95,076
    
    
    
    104,190Long-term debt
    
    
    926,078
    
    
    
    1,075,172Deferred income tax liability
    
    
    328,138
    
    
    
    293,916Total liabilities
    
    
    1,700,871
    
    
    
    1,876,566Commitments and contingencies (Note 21)Stockholders equity:Preferred stock, par value $0.01, 10,000,000 shares
authorized; no shares issued and outstanding
    
    
    
    
    
    
    Common stock, par value $0.01, 100,000,000 shares
authorized; 54,170,913 and 46,814,021 shares issued and
outstanding at December 31, 2009 and 2008, respectively
    
    
    542
    
    
    
    468Additional paid-in capital
    
    
    289,853
    
    
    
    183,642Accumulated other comprehensive loss, net of income tax
    
    
    (32,871
    )
    
    
    (37,354
    )Retained earnings
    
    
    165,248
    
    
    
    287,895Total stockholders equity
    
    
    422,772
    
    
    
    434,651Non-controlling interest in subsidiaries
    
    
    9,146
    
    
    
    17,916Preferred stock of subsidiary including accumulated dividends
    
    
    
    
    
    
    84,300Total equity
    
    
    431,918
    
    
    
    536,867Total liabilities and equity
    
    $
    2,132,789
    
    
    $
    2,413,433
  F-4




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
CONSOLIDATED STATEMENTS OF OPERATIONS
(in thousands except per share data)
 Year Ended December 31,2009
    
    
    2008
    
    
    2007Net sales (1)
    
    $
    3,915,732
    
    
    $
    5,156,706
    
    
    $
    4,542,151Operating costs and expenses:Cost of sales
    
    
    3,502,782
    
    
    
    4,853,195
    
    
    
    3,999,287Direct operating expenses
    
    
    265,502
    
    
    
    216,498
    
    
    
    201,196Selling, general and administrative expenses
    
    
    129,446
    
    
    
    119,852
    
    
    
    105,352Net costs associated with fire
    
    
    
    
    
    
    56,854
    
    
    
    Business interruption recovery
    
    
    
    
    
    
    (55,000
    )
    
    
    Depreciation and amortization
    
    
    97,247
    
    
    
    66,754
    
    
    
    57,403Total operating costs and expenses
    
    
    3,994,977
    
    
    
    5,258,153
    
    
    
    4,363,238Gain on involuntary conversion of assets
    
    
    
    
    
    
    279,680
    
    
    
    Gain (loss) on disposition of assets
    
    
    (1,591
    )
    
    
    45,244
    
    
    
    7,206Operating income (loss)
    
    
    (80,836
    )
    
    
    223,477
    
    
    
    186,119Interest expense
    
    
    (111,137
    )
    
    
    (67,550
    )
    
    
    (47,747
    )Equity earnings (losses) of investees
    
    
    24,558
    
    
    
    (1,522
    )
    
    
    11,177Other income, net
    
    
    331
    
    
    
    1,500
    
    
    
    6,565Income (loss) before income tax expense (benefit),
non-controlling interest in income (loss) of subsidiaries,
and accumulated dividends on preferred stock of subsidiary
    
    
    (167,084
    )
    
    
    155,905
    
    
    
    156,114Income tax expense (benefit)
    
    
    (64,877
    )
    
    
    62,781
    
    
    
    46,199Income (loss) before non-controlling interest in income
(loss) of subsidiaries and accumulated dividends on
preferred stock of subsidiary
    
    
    (102,207
    )
    
    
    93,124
    
    
    
    109,915Non-controlling interest in income (loss) of subsidiaries
    
    
    (8,551
    )
    
    
    5,941
    
    
    
    5,979Accumulated dividends on preferred stock of subsidiary
    
    
    21,500
    
    
    
    4,300
    
    
    
    Net income (loss) available to common stockholders
    
    $
    (115,156
    )
    
    $
    82,883
    
    
    $
    103,936Earnings (loss) per share, basic
    
    $
    (2.46
    )
    
    $
    1.77
    
    
    $
    2.22Weighted average shares outstanding, basic (in thousands)
    
    
    46,829
    
    
    
    46,788
    
    
    
    46,763Earnings (loss) per share, diluted
    
    $
    (2.46
    )
    
    $
    1.72
    
    
    $
    2.16Weighted average shares outstanding, diluted (in thousands)
    
    
    46,829
    
    
    
    49,583
    
    
    
    46,804Cash dividends per share
    
    $
    0.16
    
    
    $
    0.16
    
    
    $
    0.16
 
 (1)
    
    Includes excise taxes on sales by the retail and branded marketing segment of $47,137,
$37,483 and $35,808 for the years ended December 31, 2009, 2008, and 2007, respectively.  F-5




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
CONSOLIDATED STATEMENTS OF STOCKHOLDERS EQUITY
(dollars in thousands)
 AccumulatedAdditional
    
    
    Other
    
    
    
    
    
    
    TotalCommon
    
    
    Paid-In
    
    
    Comprehensive
    
    
    Retained
    
    
    Stockholders
    
    
    Non-controlling
    
    
    TotalStock
    
    
    Capital
    
    
    Income (Loss)
    
    
    Earnings
    
    
    Equity
    
    
    Interest (1)
    
    
    EquityBalance at December 31, 2006
    
    $
    468
    
    
    $
    181,622
    
    
    $
    (7,400
    )
    
    $
    116,056
    
    
    $
    290,746
    
    
    $
    9,116
    
    
    $
    299,862Stock compensation expense
    
    
    
    
    
    
    1,310
    
    
    
    
    
    
    
    
    
    
    
    1,310
    
    
    
    1,112
    
    
    
    2,422Dividends
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (7,490
    )
    
    
    (7,490
    )
    
    
    (468
    )
    
    
    (7,958
    )Income before non-controlling interest
in income of subsidiaries
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    103,936
    
    
    
    103,936
    
    
    
    5,979
    
    
    
    109,915Other comprehensive income (loss):Defined benefit pension plans, net of
tax of $958
    
    
    
    
    
    
    
    
    
    
    1,532
    
    
    
    
    
    
    
    1,532
    
    
    
    99
    
    
    
    1,631Fair value of interest rate swaps,
net of tax of $1,050
    
    
    
    
    
    
    
    
    
    
    (1,832
    )
    
    
    
    
    
    
    (1,832
    )
    
    
    (118
    )
    
    
    (1,950
    )Total comprehensive income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    103,636
    
    
    
    5,960
    
    
    
    109,596Balance at December 31, 2007
    
    
    468
    
    
    
    182,932
    
    
    
    (7,700
    )
    
    
    212,502
    
    
    
    388,202
    
    
    
    15,720
    
    
    
    403,922Stock compensation expense
    
    
    
    
    
    
    710
    
    
    
    
    
    
    
    
    
    
    
    710
    
    
    
    (1,062
    )
    
    
    (352
    )Dividends
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (7,490
    )
    
    
    (7,490
    )
    
    
    (386
    )
    
    
    (7,876
    )Sale of preferred stock by subsidiary (1)
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    80,000
    
    
    
    80,000Income before non-controlling interest
in income of subsidiaries and
accumulated dividends on preferred stock
of subsidiary (1)
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    82,883
    
    
    
    82,883
    
    
    
    10,241
    
    
    
    93,124Other comprehensive income (loss):Defined benefit pension plans, net of
tax of $8,780
    
    
    
    
    
    
    
    
    
    
    (13,481
    )
    
    
    
    
    
    
    (13,481
    )
    
    
    (1,044
    )
    
    
    (14,525
    )Fair value of commodity derivative
contracts, net of tax of $677
    
    
    
    
    
    
    
    
    
    
    (1,071
    )
    
    
    
    
    
    
    (1,071
    )
    
    
    (83
    )
    
    
    (1,154
    )Fair value of interest rate swaps,
net of tax of $6,828
    
    
    
    
    
    
    
    
    
    
    (15,102
    )
    
    
    
    
    
    
    (15,102
    )
    
    
    (1,170
    )
    
    
    (16,272
    )Total comprehensive income
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    53,229
    
    
    
    7,944
    
    
    
    61,173Balance at December 31, 2008
    
    
    468
    
    
    
    183,642
    
    
    
    (37,354
    )
    
    
    287,895
    
    
    
    434,651
    
    
    
    102,216
    
    
    
    536,867Stock compensation expense
    
    
    
    
    
    
    485
    
    
    
    
    
    
    
    
    
    
    
    485
    
    
    
    17
    
    
    
    502Dividends
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (7,491
    )
    
    
    (7,491
    )
    
    
    (576
    )
    
    
    (8,067
    )Conversion of preferred stock of
subsidiary for common stock
    
    
    74
    
    
    
    105,726
    
    
    
    
    
    
    
    
    
    
    
    105,800
    
    
    
    (105,800
    )
    
    
    Income (loss) before non-controlling
interest in income (loss) of
subsidiaries and accumulated dividends
on preferred stock of subsidiary (1)
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (115,156
    )
    
    
    (115,156
    )
    
    
    12,949
    
    
    
    (102,207
    )Other comprehensive income (loss):Defined benefit pension plans, plus
tax of $887
    
    
    
    
    
    
    
    
    
    
    2,110
    
    
    
    
    
    
    
    2,110
    
    
    
    162
    
    
    
    2,272Fair value of commodity derivative
contracts, net of tax of $2,000
    
    
    
    
    
    
    
    
    
    
    (3,166
    )
    
    
    
    
    
    
    (3,166
    )
    
    
    (243
    )
    
    
    (3,409
    )Fair value of interest rate swaps,
net of tax of $3,207
    
    
    
    
    
    
    
    
    
    
    5,539
    
    
    
    
    
    
    
    5,539
    
    
    
    421
    
    
    
    5,960Total comprehensive income (loss)
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (110,673
    )
    
    
    13,289
    
    
    
    (97,384
    )Balance at December 31, 2009
    
    $
    542
    
    
    $
    289,853
    
    
    $
    (32,871
    )
    
    $
    165,248
    
    
    $
    422,772
    
    
    $
    9,146
    
    
    $
    431,918
 
 (1)
    
    Includes $80,000 in sale of preferred stock by subsidiary in connection with the Krotz
Springs refinery acquisition in July 2008 and accumulated dividends of $21,500 and $4,300
through December 31, 2009 and 2008, respectively.  F-6




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
CONSOLIDATED STATEMENTS OF CASH FLOWS
(dollars in thousands)
 Year Ended December 31,2009
    
    
    2008
    
    
    2007Cash flows from operating activities:Net income (loss) available to common stockholders
    
    $
    (115,156
    )
    
    $
    82,883
    
    
    $
    103,936Adjustments to reconcile net income (loss) available to common
stockholders to cash provided by (used in) operating activities:Depreciation and amortization
    
    
    97,247
    
    
    
    66,754
    
    
    
    57,403Stock compensation
    
    
    502
    
    
    
    173
    
    
    
    2,264Deferred income tax expense (benefit)
    
    
    (5,451
    )
    
    
    177,797
    
    
    
    (2,984
    )Non-controlling interest in income (loss) of subsidiaries
    
    
    (8,551
    )
    
    
    5,941
    
    
    
    5,979Accumulated dividends on preferred stock of subsidiary
    
    
    21,500
    
    
    
    4,300
    
    
    
    Equity (earnings) losses of investees (net of dividends)
    
    
    (5,391
    )
    
    
    4,296
    
    
    
    (1,876
    )Amortization of debt issuance costs
    
    
    7,112
    
    
    
    4,128
    
    
    
    2,093Amortization of original issuance discount
    
    
    328
    
    
    
    
    
    
    
    Write-off of unamortized debt issuance costs
    
    
    20,482
    
    
    
    
    
    
    
    Mark-to-market of heating oil hedge
    
    
    
    
    
    
    (117,452
    )
    
    
    Gain on involuntary conversion of assets
    
    
    
    
    
    
    (279,680
    )
    
    
    (Gain) loss on disposition of assets
    
    
    1,591
    
    
    
    (45,244
    )
    
    
    (7,206
    )Changes in operating assets and liabilities, net of acquisition effects:Accounts and other receivables, net
    
    
    67,357
    
    
    
    59,336
    
    
    
    (144,068
    )Income tax receivable
    
    
    51,146
    
    
    
    (81,320
    )
    
    
    Inventories
    
    
    17,321
    
    
    
    213,373
    
    
    
    16,715Heating oil crack spread hedge
    
    
    117,485
    
    
    
    
    
    
    
    Prepaid expenses and other current assets
    
    
    2,164
    
    
    
    5,933
    
    
    
    794Other assets
    
    
    5,992
    
    
    
    (5,264
    )
    
    
    7,561Accounts payable
    
    
    40,892
    
    
    
    (108,458
    )
    
    
    82,141Accrued liabilities
    
    
    (25,197
    )
    
    
    17,419
    
    
    
    8,312Other non-current liabilities
    
    
    (8,228
    )
    
    
    (5,727
    )
    
    
    (7,114
    )Net cash provided by (used in) operating activities
    
    
    283,145
    
    
    
    (812
    )
    
    
    123,950Cash flows from investing activities:Capital expenditures
    
    
    (81,660
    )
    
    
    (62,356
    )
    
    
    (42,204
    )Capital expenditures to rebuild the Big Spring refinery
    
    
    (46,769
    )
    
    
    (362,178
    )
    
    
    Capital expenditures for turnarounds and catalysts
    
    
    (24,699
    )
    
    
    (9,958
    )
    
    
    (9,842
    )Proceeds from insurance to rebuild the Big Spring refinery
    
    
    34,125
    
    
    
    270,885
    
    
    
    Proceeds from disposition of assets
    
    
    
    
    
    
    7,000
    
    
    
    Earnout payments related to Krotz Springs refinery acquisition
    
    
    (19,688
    )
    
    
    
    
    
    
    Sale (purchase) of short-term investments, net
    
    
    
    
    
    
    27,296
    
    
    
    (27,296
    )Acquisition of Krotz Springs refinery
    
    
    
    
    
    
    (481,011
    )
    
    
    Acquisition of Skinnys, Inc. stock
    
    
    
    
    
    
    
    
    
    
    (75,329
    )Acquisition of Paramount Petroleum Corporation stock
    
    
    
    
    
    
    
    
    
    
    7,417Net cash used in investing activities
    
    
    (138,691
    )
    
    
    (610,322
    )
    
    
    (147,254
    )Cash flows from financing activities:Dividends paid to non-controlling interest shareholders
    
    
    (576
    )
    
    
    (386
    )
    
    
    (468
    )Dividends paid to shareholders
    
    
    (7,491
    )
    
    
    (7,490
    )
    
    
    (7,490
    )Proceeds from sale of preferred stock by subsidiary
    
    
    
    
    
    
    80,000
    
    
    
    Cash received from inventory supply agreement
    
    
    20,237
    
    
    
    
    
    
    
    Deferred debt issuance costs
    
    
    (17,768
    )
    
    
    (28,105
    )
    
    
    (2,235
    )Revolving credit facilities, net
    
    
    (60,241
    )
    
    
    276,818
    
    
    
    Additions to long-term debt
    
    
    205,365
    
    
    
    252,000
    
    
    
    46,334Payments on long-term debt
    
    
    (261,997
    )
    
    
    (11,864
    )
    
    
    (8,388
    )Net cash provided by (used in) financing activities
    
    
    (122,471
    )
    
    
    560,973
    
    
    
    27,753Net increase (decrease) in cash and cash equivalents
    
    
    21,983
    
    
    
    (50,161
    )
    
    
    4,449Cash and cash equivalents, beginning of period
    
    
    18,454
    
    
    
    68,615
    
    
    
    64,166Cash and cash equivalents, end of period
    
    $
    40,437
    
    
    $
    18,454
    
    
    $
    68,615
  F-7




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
CONSOLIDATED STATEMENTS OF CASH FLOWS
(dollars in thousands)
 Year Ended December 31,2009
    
    
    2008
    
    
    2007Supplemental cash flow information:Cash paid for interest, net of capitalized interest
    
    $
    87,164
    
    
    $
    58,504
    
    
    $
    48,686Cash (received) paid for income tax, net of refunds
    
    $
    (111,791
    )
    
    $
    (30,334
    )
    
    $
    91,781Non-cash activities:Financing activity  payments on long-term debt from
deposit held to secure heating oil crack spread hedge
    
    $
    50,000
    
    
    $
    
    
    
    $
    Financing activity  proceeds from borrowings
retained by bank as deposit for hedge related
activities for Krotz Springs refinery acquisition
    
    $
    
    
    
    $
    50,000
    
    
    $
    
  F-8




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (1) Description and Nature of Business
   Refining and Unbranded Marketing Segment
    Asphalt Segment
  F-9




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 Retail and Branded Marketing Segment
 (2) Summary of Significant Accounting Policies
 (a) Basis of Presentation
  (b) Adoption of New Accounting Standards
 Non-controlling Interests in Consolidated Financial Statements, an Amendment of ARB 51
 (w) New Accounting
Standards and Disclosures
 (c) Use of Estimates
  (d) Revenue Recognition
   F-10




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
    (e) Cost Classifications
     (f) Cash and Cash Equivalents
  (g) Accounts Receivable
  (h) Inventories
  F-11




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (i) Hedging Activity
   (j) HEP Investment
  (k) Property, Plant, and Equipment
     (l) Impairment of Long-Lived Assets and Assets To Be Disposed Of
  F-12




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (m) Asset Retirement Obligations
 Accounting for Asset Retirement Obligations Accounting for Conditional Retirement Obligations
 (n) Turnarounds and Chemical Catalyst Costs
  (o) Income Taxes
  (p) Stock-Based Compensation
    F-13




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (q) Environmental Expenditures
   (r) Earnings Per Share
  (s) Other Comprehensive Income (Loss)
  (t) Defined Benefit Pension and Other Postretirement Plans
  (u) Commitments and Contingencies
  (v) Goodwill and Intangible Assets
  F-14




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (w) New Accounting Standards and Disclosures
 The FASB Accounting Standards Codification and the
Hierarchy of Generally Accepted Accounting Principles a replacement of FASB Statement No. 162
 Subsequent Events
 Employers Disclosures about
Postretirement Benefit Plans Employers Disclosures about Pensions and Other Postretirement Benefits
 Equity Method Investment Accounting Considerations
 Accounting by Lessees
for Maintenance Deposits
 Determination of the Useful Life
of Intangible Assets Goodwill and Other Intangible Assets.
 Disclosure about Derivative Instruments and
Hedging Activities
 F-15




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Fair Value
Measurements
 Partial Deferral of the
Effective Date of Statement 157
    December 31,
    
    
    
    
    
    
    December 31,2008
    
    
    Adjustments
    
    
    2008(as previouslyreported)
    
    
    
    
    
    (recast)Total stockholders equity
    
    $
    431,919
    
    
    $
    2,732
    
    
    $
    434,651Non-controlling interest in subsidiaries (1)
    
    
    
    
    
    
    17,916
    
    
    
    17,916Preferred stock of subsidiary including accumulated dividends (1)
    
    
    
    
    
    
    84,300
    
    
    
    84,300Total equity
    
    $
    431,919
    
    
    $
    104,948
    
    
    $
    536,867
 
 (1)
    
    Previously reported outside of equity.  Business Combinations
 F-16




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (x) Reclassifications
  (3) Big Spring Refinery Fire
      (4) Acquisition s
 Krotz Springs Refinery Acquisition
    F-17




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   Cash paid
    
    $
    474,494Transaction costs
    
    
    6,517Total Purchase Price
    
    $
    481,011
  Current assets
    
    $
    145,859Property, plant and equipment
    
    
    376,702Current liabilities
    
    
    (29,309
    )Other non-current liabilities
    
    
    (12,241
    )Total Purchase Price
    
    $
    481,011
   Unaudited Pro Forma Financial Information
  
    
    The acquisition of the Krotz Springs refining business occurred on January 1, 2008;
    
    $302,000 of term debt and $141,494 of borrowings under the revolving credit facility
was incurred on January 1, 2008 to fund the acquisition and buy initial inventories; and
    
    Depreciation expense was higher beginning January 1, 2008 based upon the revaluation of
estimated asset values as of that date.
 F-18




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 
 Year EndedDecember 31,2009
    
    
    2008(pro forma)Net sales
    
    $
    3,915,732
    
    
    $
    6,696,335Operating income (loss)
    
    
    (80,836
    )
    
    
    167,096Net income (loss) available to common stockholders
    
    
    (115,156
    )
    
    
    31,027Earnings (loss) per share, basic
    
    $
    (2.46
    )
    
    $
    0.66Earnings (loss) per share, diluted
    
    $
    (2.46
    )
    
    $
    0.66
 (5) Contribution and Sale of Pipelines and Terminals
 HEP Transaction
    (6) Segment Data
  (a) Refining and Unbranded Marketing Segment
  F-19




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (b) Asphalt Segment
  (c) Retail and Branded Marketing Segment
  (d) Corporate
   Refining and
    
    
    
    
    
    Retail andUnbranded
    
    
    
    
    
    Branded
    
    
    
    
    
    ConsolidatedYear ended December 31, 2009
    
    Marketing
    
    Asphalt
    
    Marketing
    
    Corporate
    
    TotalNet sales to external customers
    
    $
    2,666,596
    
    
    $
    440,915
    
    
    $
    808,221
    
    
    $
    
    
    
    $
    3,915,732Intersegment sales/purchases
    
    
    692,447
    
    
    
    (233,212
    )
    
    
    (459,235
    )
    
    
    
    
    
    
    Depreciation and amortization
    
    
    76,252
    
    
    
    6,807
    
    
    
    13,464
    
    
    
    724
    
    
    
    97,247Operating income (loss)
    
    
    (86,533
    )
    
    
    (654
    )
    
    
    7,832
    
    
    
    (1,481
    )
    
    
    (80,836
    )Total assets
    
    
    1,757,436
    
    
    
    172,995
    
    
    
    185,185
    
    
    
    17,173
    
    
    
    2,132,789Capital expenditures to rebuild the
Big Spring refinery
    
    
    46,769
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    46,769Turnaround, chemical catalyst and
capital expenditures
    
    
    96,254
    
    
    
    2,579
    
    
    
    3,822
    
    
    
    3,704
    
    
    
    106,359
 F-20




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 Refining and
    
    
    
    
    
    Retail andUnbranded
    
    
    
    
    
    Branded
    
    
    
    
    
    ConsolidatedYear ended December 31, 2008
    
    Marketing
    
    Asphalt
    
    Marketing
    
    Corporate
    
    TotalNet sales to external customers
    
    $
    3,282,166
    
    
    $
    647,221
    
    
    $
    1,227,319
    
    
    $
    
    
    
    $
    5,156,706Intersegment sales/purchases
    
    
    1,269,603
    
    
    
    (369,505
    )
    
    
    (900,098
    )
    
    
    
    
    
    
    Depreciation and amortization
    
    
    50,047
    
    
    
    2,139
    
    
    
    13,674
    
    
    
    894
    
    
    
    66,754Operating income (loss)
    
    
    128,772
    
    
    
    97,442
    
    
    
    (1,239
    )
    
    
    (1,498
    )
    
    
    223,477Total assets
    
    
    1,973,324
    
    
    
    231,921
    
    
    
    193,815
    
    
    
    14,373
    
    
    
    2,413,433Capital expenditures to rebuild the Big
Spring refinery
    
    
    362,178
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    362,178Turnaround, chemical catalyst and
capital expenditures
    
    
    67,534
    
    
    
    644
    
    
    
    2,928
    
    
    
    1,208
    
    
    
    72,314Refining and
    
    
    
    
    
    Retail andUnbranded
    
    
    
    
    
    Branded
    
    
    
    
    
    ConsolidatedYear ended December 31, 2007
    
    Marketing
    
    Asphalt
    
    Marketing
    
    Corporate
    
    TotalNet sales to external customers
    
    $
    2,624,698
    
    
    $
    642,937
    
    
    $
    1,274,516
    
    
    $
    
    
    
    $
    4,542,151Intersegment sales/purchases
    
    
    1,465,909
    
    
    
    (502,924
    )
    
    
    (962,985
    )
    
    
    
    
    
    
    Depreciation and amortization
    
    
    44,107
    
    
    
    2,145
    
    
    
    10,245
    
    
    
    906
    
    
    
    57,403Operating income (loss)
    
    
    165,073
    
    
    
    (1,671
    )
    
    
    24,146
    
    
    
    (1,429
    )
    
    
    186,119Total assets
    
    
    1,086,020
    
    
    
    238,423
    
    
    
    237,015
    
    
    
    19,928
    
    
    
    1,581,386Turnaround, chemical catalyst and
capital expenditures
    
    
    38,511
    
    
    
    2,167
    
    
    
    9,797
    
    
    
    1,571
    
    
    
    52,046
   (7) Fair Value
   F-21




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Quoted PricesinActive Markets
    
    Significantfor Identical
    
    Other
    
    SignificantAssets or
    
    Observable
    
    UnobservableLiabilities
    
    Inputs
    
    Inputs
    
    ConsolidatedYear ended December 31, 2009
    
    (Level 1)
    
    (Level 2)
    
    (Level 3)
    
    TotalAssets:Futures and forwards
    
    $
    322
    
    
    $
    
    
    
    $
    
    
    
    $
    322Commodity swaps
    
    
    
    
    
    
    89
    
    
    
    
    
    
    
    89Liabilities:Commodity swaps
    
    
    
    
    
    
    9,983
    
    
    
    
    
    
    
    9,983Interest rate swaps
    
    
    
    
    
    
    16,933
    
    
    
    
    
    
    
    16,933Year ended
December 31, 2008Assets:Commodity swaps
    
    $
    
    
    
    $
    117,485
    
    
    $
    
    
    
    $
    117,485Liabilities:Futures and forwards
    
    
    1,197
    
    
    
    
    
    
    
    
    
    
    
    1,197Commodity swaps
    
    
    
    
    
    
    25,473
    
    
    
    
    
    
    
    25,473Interest rate swaps
    
    
    
    
    
    
    26,100
    
    
    
    
    
    
    
    26,100
 (8) Derivative Instruments
 Commodity Derivatives  Mark to Market
       F-22




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
     Cash Flow Hedges
  Interest Rate Derivatives.
   Commodity Derivatives.
 F-23




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
    December 31,Counterparty Credit Quality (1)
    
    2009AAA
    
    $
    322AA
    
    
    (17,856
    )A
    
    
    (8,971
    )Lower than A
    
    
    Total
    
    $
    (26,505
    )
 
 (1)
    
    As determined by nationally recognized statistical ratings organizations.  As of December 31, 2009Asset Derivatives
    
    
    Liability DerivativesBalance Sheet
    
    
    
    
    
    
    Balance SheetLocation
    
    
    Fair Value
    
    
    Location
    
    
    Fair ValueDerivatives not
designated as
hedging instruments
under FAS 133:Commodity contracts
(futures, forwards
and SPR swaps)
    
    Accounts receivable
    
    $
    411
    
    
    Accrued liabilities
    
    $
    (9,983
    )Total derivatives
not designated as
hedging instruments
under FAS 133
    
    
    
    
    
    $
    411
    
    
    
    
    
    
    $
    (9,983
    )Derivatives
designated as
hedging instruments
under FAS 133:Interest rate swaps
    
    
    
    
    
    $
    
    
    
    Other non-current liabilities
    
    $
    (16,933
    )Total derivatives
designated as
hedging instruments
under FAS 133
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (16,933
    )Total derivatives
    
    
    
    
    
    $
    411
    
    
    
    
    
    
    $
    (26,916
    )
 F-24




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Gain (Loss) Reclassifiedfrom Accumulated OCI intoIncome (IneffectiveGain (Loss) Reclassified from
    
    
    Portion and AmountCash Flow Hedging
    
    Gain (Loss)
    
    
    Accumulated OCI into Income
    
    
    Excluded fromRelationships
    
    Recognized in OCI
    
    
    (Effective Portion)
    
    
    Effectiveness Testing)Location
    
    
    Amount
    
    
    Location
    
    
    AmountFor the Year Ended
December 31, 2009Commodity swaps
(heating oil
swaps)
    
    $
    
    
    
    Cost of sales
    
    $
    5,409
    
    
    
    
    
    
    $
    Interest rate swaps
    
    
    9,167
    
    
    Interest expense
    
    
    (14,590
    )
    
    
    
    
    
    
    Total derivatives
    
    $
    9,167
    
    
    
    
    
    
    $
    (9,181
    )
    
    
    
    
    
    $
    
 Derivatives not designated as hedging instruments  under FAS 133:
 Gain (Loss) Recognized in IncomeLocation
    
    
    AmountFor the Year Ended
December 31, 2009Commodity contracts (futures & forwards)
    
    Cost of sales
    
    $
    (14,325
    )Commodity contracts (heating oil swaps)
    
    Cost of sales
    
    
    48,956Commodity contracts (SPR swaps)
    
    Cost of sales
    
    
    (11,058
    )Total derivatives
    
    
    
    
    
    $
    23,573
 (9) Accounts and Other Receivables
   December 31,2009
    
    
    2008Trade accounts receivable
    
    $
    115,063
    
    
    $
    172,513Insurance receivable
    
    
    
    
    
    
    34,125Other receivables
    
    
    11,898
    
    
    
    18,782Total accounts and other receivables
    
    $
    126,961
    
    
    $
    225,420
  F-25




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Balance at
    
    AdditionsBeginning of
    
    Charged to
    
    
    
    
    
    Balance at EndPeriod
    
    Expense (1)
    
    Deductions (2)
    
    of Period(amounts in thousands)Allowance for doubtful accounts:2009
    
    $
    20,844
    
    
    
    3,300
    
    
    
    (277
    )
    
    $
    23,8672008
    
    $
    1,593
    
    
    
    20,122
    
    
    
    (871
    )
    
    $
    20,8442007
    
    $
    1,251
    
    
    
    161
    
    
    
    181
    
    
    $
    1,593
 
 (1)
    
    Substantially all of the additions charged to expense in 2009 and 2008 relate to the SEMGroup,
LP bankruptcy.(2)
    
    Amounts written off net of recoveries. (10) Inventories
   December 31,2009
    
    
    2008Crude oil, refined products, asphalt and blendstocks
    
    $
    150,370
    
    
    $
    192,997Crude oil, inventory consigned to others
    
    
    22,558
    
    
    
    Materials and supplies
    
    
    18,069
    
    
    
    16,456Store merchandise
    
    
    18,856
    
    
    
    19,875Store fuel
    
    
    5,146
    
    
    
    2,992Total inventories
    
    $
    214,999
    
    
    $
    232,320
   (11) Property, Plant, and Equipment, Net
  December 31,2009
    
    
    2008Refining facilities
    
    $
    1,535,841
    
    
    $
    1,430,896Pipelines and terminals
    
    
    39,213
    
    
    
    39,161Retail
    
    
    137,150
    
    
    
    134,263Other
    
    
    16,747
    
    
    
    13,052Property, plant and equipment, gross
    
    
    1,728,951
    
    
    
    1,617,372Less accumulated depreciation
    
    
    (251,525
    )
    
    
    (168,413
    )Property, plant and equipment, net
    
    $
    1,477,426
    
    
    $
    1,448,959
 F-26




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Refining facilities
    
    3  20 years; average 18 yearsPipelines and terminals
    
    5  25 years; average 23 yearsRetail
    
    5  40 years; average 8 yearsOther
    
    3  15 years; average 5 years
  (12) Other Assets
  December 31,2009
    
    
    2008Deferred turnaround and chemical catalyst cost
    
    $
    24,387
    
    
    $
    11,684Environmental receivables
    
    
    3,448
    
    
    
    8,524Deferred debt issuance costs
    
    
    25,822
    
    
    
    35,648Intangible assets
    
    
    8,516
    
    
    
    7,055Deposit for hedge related activities for Krotz Springs refinery acquisition
    
    
    
    
    
    
    50,000Commodity swaps
    
    
    
    
    
    
    42,080Other
    
    
    8,359
    
    
    
    12,207Total other assets
    
    $
    70,532
    
    
    $
    167,198
   F-27




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (13) Accrued Liabilities and Other Non-Current Liabilities
  December 31,2009
    
    
    2008Accrued Liabilities:Taxes other than income taxes, primarily excise taxes
    
    $
    20,205
    
    
    $
    27,789Employee costs
    
    
    6,716
    
    
    
    4,884Commodity swaps
    
    
    9,983
    
    
    
    26,670Valero earnout liability (Note 4)
    
    
    8,750
    
    
    
    Other
    
    
    46,726
    
    
    
    51,974Total accrued liabilities
    
    $
    92,380
    
    
    $
    111,317Other Non-Current Liabilities:Pension and other postemployment benefit liabilities, net (Note 14)
    
    $
    34,902
    
    
    $
    35,989Environmental accrual (Note 21)
    
    
    27,350
    
    
    
    33,181Asset retirement obligations
    
    
    8,789
    
    
    
    8,386Interest rate swap valuations
    
    
    16,933
    
    
    
    26,100Valero earnout liability (Note 4)
    
    
    6,562
    
    
    
    Other
    
    
    540
    
    
    
    534Total other non-current liabilities
    
    $
    95,076
    
    
    $
    104,190
    December 31,2009
    
    
    2008Balance at beginning of year
    
    $
    8,386
    
    
    $
    7,378Accretion expense
    
    
    421
    
    
    
    342Additional accretion due to change in risk free interest rate
    
    
    
    
    
    
    Retirements
    
    
    (90
    )
    
    
    (150
    )Additions
    
    
    72
    
    
    
    816Balance at end of year
    
    $
    8,789
    
    
    $
    8,386
  (14) Employee and Postretirement Benefits
 (a) Retirement Plans
  F-28




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
   Pension Benefits2009
    
    
    2008Change in projected benefit obligation:Benefit obligation at beginning of year
    
    $
    56,213
    
    
    $
    45,409Service cost
    
    
    3,347
    
    
    
    2,307Interest cost
    
    
    3,362
    
    
    
    2,889Plan participants contributions
    
    
    
    
    
    
    Plan amendments
    
    
    
    
    
    
    276Actuarial loss (gain)
    
    
    3,467
    
    
    
    6,767Benefits paid
    
    
    (1,616
    )
    
    
    (1,435
    )Projected benefit obligations at end of year
    
    $
    64,773
    
    
    $
    56,213Change in plan assets:Fair value of plan assets at beginning of year
    
    
    23,834
    
    
    
    35,324Actual (loss) gain on plan assets
    
    
    7,100
    
    
    
    (13,380
    )Employer contribution
    
    
    4,165
    
    
    
    3,325Plan participants contributions
    
    
    
    
    
    
    Benefits paid
    
    
    (1,616
    )
    
    
    (1,435
    )Fair value of plan assets at end of year
    
    $
    33,483
    
    
    $
    23,834Reconciliation of funded status:Fair value of plan assets at end of year
    
    $
    33,483
    
    
    $
    23,834Less projected benefit obligations at end of year
    
    
    64,773
    
    
    
    56,213Under-funded status at end of year
    
    $
    (31,290
    )
    
    $
    (32,379
    )
  Pension Benefits2009
    
    
    2008Amounts recognized in the consolidated balance sheets:Pension benefit liability
    
    $
    (31,290
    )
    
    $
    (32,379
    )
  Pension Benefits2009
    
    
    2008Net actuarial loss
    
    $
    (32,178
    )
    
    $
    (33,563
    )Prior service credit
    
    
    545
    
    
    
    603Total
    
    $
    (31,633
    )
    
    $
    (32,960
    )
  PensionBenefitsAmortization of prior service cost (credit)
    
    $
    (58
    )Amortization of loss
    
    
    1,599Total
    
    $
    1,541
 F-29




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  December 31,2009
    
    2008Projected benefit obligation
    
    $
    64,773
    
    
    $
    56,213Accumulated benefit obligation
    
    
    58,022
    
    
    
    48,460Fair value of plan assets
    
    
    33,483
    
    
    
    23,834
  Pension Benefits2009
    
    2008
    
    2007Discount rate
    
    
    5.93
    %
    
    
    6.07
    %
    
    
    6.46
    %Rate of compensation increase
    
    
    2.50
    %
    
    
    3.50
    %
    
    
    3.50
    %
   Pension Benefits2009
    
    2008
    
    2007Discount rate
    
    
    6.07
    %
    
    
    6.46
    %
    
    
    5.75
    %Expected return on plan assets
    
    
    9.00
    %
    
    
    9.00
    %
    
    
    9.00
    %Rate of compensation increase
    
    
    3.50
    %
    
    
    3.50
    %
    
    
    3.50
    %
  Pension BenefitsYear Ended December 312009
    
    
    2008
    
    
    2007Components of net periodic benefit cost:Service cost
    
    $
    3,347
    
    
    $
    2,307
    
    
    $
    1,979Interest cost
    
    
    3,362
    
    
    
    2,889
    
    
    
    2,568Amortization of prior service costs
    
    
    (58
    )
    
    
    (78
    )
    
    
    (41
    )Expected return on plan assets
    
    
    (3,359
    )
    
    
    (3,284
    )
    
    
    (2,809
    )Recognized net actuarial loss
    
    
    1,109
    
    
    
    481
    
    
    
    766Net periodic benefit cost
    
    $
    4,401
    
    
    $
    2,315
    
    
    $
    2,463
 Plan Assets
  Pension BenefitsPlan Assets2009
    
    2008Asset Category:Equity securities
    
    
    78.0
    %
    
    
    74.0
    %Debt securities
    
    
    13.0
    %
    
    
    16.0
    %Real estate investment trust
    
    
    9.0
    %
    
    
    10.0
    %Total
    
    
    100.0
    %
    
    
    100.0
    %
 F-30




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Quoted PricesinActive Markets
    
    
    Significantfor Identical
    
    
    Other
    
    
    SignificantAssets or
    
    
    Observable
    
    
    UnobservableLiabilities
    
    
    Inputs
    
    
    Inputs
    
    
    ConsolidatedYear ended December 31, 2009
    
    (Level 1)
    
    
    (Level 2)
    
    
    (Level 3)
    
    
    TotalEquity securities:U.S companies
    
    $
    20,658
    
    
    $
    
    
    
    $
    
    
    
    $
    20,658International companies
    
    
    5,488
    
    
    
    
    
    
    
    
    
    
    
    5,488Debt securities:Preferred securities
    
    
    2,118
    
    
    
    
    
    
    
    
    
    
    
    2,118Bond & mortgage backed securities
    
    
    
    
    
    
    2,197
    
    
    
    
    
    
    
    2,197Real estate securities
    
    
    3,022
    
    
    
    
    
    
    
    
    
    
    
    3,022Total
    
    $
    31,286
    
    
    $
    2,197
    
    
    $
    
    
    
    $
    33,483
  Cash Flows
      (b) Postretirement Medical Plan
   F-31




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (15) Long-Term Debt
  December 31,2009
    
    
    2008Term loan credit facilities
    
    $
    434,250
    
    
    $
    739,810Revolving credit facilities
    
    
    216,577
    
    
    
    276,818Senior secured notes
    
    
    205,693
    
    
    
    Retail credit facilities
    
    
    80,504
    
    
    
    86,941Total debt
    
    
    937,024
    
    
    
    1,103,569Less current portion
    
    
    (10,946
    )
    
    
    (28,397
    )Total long-term debt
    
    $
    926,078
    
    
    $
    1,075,172
 (a) Alon USA Energy, Inc. Credit Facilities
 Term Loan Credit Facility
     Letters
of Credit Facilities.
   (b) Alon USA, LP Credit Facilities
 Revolving Credit Facility.
   F-32




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
    (c) Paramount Petroleum Corporation Credit Facility
 Revolving Credit Facility.
     (d) Alon Refining Krotz Springs, Inc. Credit Facilities
 Term Loan Credit Facility
    Senior Secured Notes.
 F-33




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
        Revolving Credit Facility.
      F-34




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
    (e) Retail Credit Facilities
      (f) Other Retail Related Credit Facilities
  (g) Maturity of Long-Term Debt
  F-35




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (h) Interest and Financing Expense
  December 31,2009
    
    
    2008
    
    
    2007Interest expense
    
    $
    63,627
    
    
    $
    56,706
    
    
    $
    39,559Letters of credit and finance charges
    
    
    21,280
    
    
    
    10,133
    
    
    
    6,095Amortization of debt issuance costs
(includes write-off of unamortized debt
issuance costs in 2009 of $20,482)
    
    
    27,594
    
    
    
    4,128
    
    
    
    2,093Amortization of original issuance discount
    
    
    328
    
    
    
    
    
    
    
    Capitalized interest
    
    
    (1,692
    )
    
    
    (3,417
    )
    
    
    Total interest expense
    
    $
    111,137
    
    
    $
    67,550
    
    
    $
    47,747
 16) Income Taxes
  December 31,2009
    
    
    2008
    
    
    2007Current:Federal
    
    $
    (60,282
    )
    
    $
    (117,679
    )
    
    $
    49,237State
    
    
    856
    
    
    
    2,663
    
    
    
    (54
    )Total current
    
    
    (59,426
    )
    
    
    (115,016
    )
    
    
    49,183Deferred:Federal
    
    
    4,675
    
    
    
    170,869
    
    
    
    (2,762
    )State
    
    
    (10,126
    )
    
    
    6,928
    
    
    
    (222
    )Total deferred
    
    
    (5,451
    )
    
    
    177,797
    
    
    
    (2,984
    )Income tax expense (benefit)
    
    $
    (64,877
    )
    
    $
    62,781
    
    
    $
    46,199
  December 31,2009
    
    
    2008
    
    
    2007Computed expected tax expense (benefit)
    
    $
    (58,479
    )
    
    $
    54,567
    
    
    $
    54,640State and local income taxes, net of federal benefit
    
    
    (6,705
    )
    
    
    6,234
    
    
    
    (4,960
    )Deduction for qualified production income
    
    
    1,972
    
    
    
    4,343
    
    
    
    (3,403
    )Other, net
    
    
    (1,665
    )
    
    
    (2,363
    )
    
    
    (78
    )Income tax expense (benefit)
    
    $
    (64,877
    )
    
    $
    62,781
    
    
    $
    46,199
  F-36




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  December 31,2009
    
    
    2008Deferred income tax assets:Accounts receivable, allowance
    
    $
    212
    
    
    $
    352Accrued liabilities and other
    
    
    2,720
    
    
    
    10,735Post retirement benefits
    
    
    13,262
    
    
    
    12,416Non-current accrued liabilities and other
    
    
    23,003
    
    
    
    4,125Net operating loss carryover
    
    
    23,337
    
    
    
    17,062Tax credits
    
    
    1,815
    
    
    
    1,583Other
    
    
    612
    
    
    
    736Deferred income tax assets
    
    
    64,961
    
    
    
    47,009Deferred income tax liabilities:Deferred charges
    
    
    (91
    )
    
    
    (1,938
    )Unrealized Gains
    
    
    (33,725
    )
    
    
    (54,556
    )Property, plant, and equipment
    
    
    (333,107
    )
    
    
    (289,959
    )Other non-current
    
    
    (8,070
    )
    
    
    (9,957
    )Inventories
    
    
    (6,226
    )
    
    
    (15,085
    )Intangibles
    
    
    (4,180
    )
    
    
    Deferred income tax liabilities
    
    $
    (385,399
    )
    
    $
    (371,495
    )
    (17) Related-Party Transactions
 (a) Consulting Agreement
  F-37




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
 (b) Sale of Preferred Shares
       F-38




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  (18) Stockholders Equity
 (a) Common and preferred stock
   CommonStock(in thousands)Balance as of December 31, 2007
    
    
    46,808Shares forfeited
    
    
    Shares issued in connection with stock plans (Note 20)
    
    
    6Balance as of December 31, 2008
    
    
    46,814Shares forfeited
    
    
    Shares issued in connection with stock plans (Note 20)
    
    
    6Shares exchanged for preferred stock of subsidiary (Note 17)
    
    
    7,351Balance as of December 31, 2009
    
    
    54,171
 (b) Dividends
    (19) Earnings per Share
  F-39




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  December 312009
    
    
    2008
    
    
    2007Net income (loss) available to common stockholders
    
    $
    (115,156
    )
    
    $
    82,883
    
    
    $
    103,936Average number of shares of common stock outstanding
    
    
    46,829
    
    
    
    46,788
    
    
    
    46,763Dilutive restricted shares, SARs, and convertible preferred shares
    
    
    
    
    
    
    2,795
    
    
    
    41Average number of shares of common stock outstanding assuming
dilution
    
    
    46,829
    
    
    
    49,583
    
    
    
    46,804Earnings per share  basic
    
    $
    (2.46
    )
    
    $
    1.77
    
    
    $
    2.22Earnings per share  diluted *
    
    $
    (2.46
    )
    
    $
    1.72
    
    
    $
    2.16
 
 *
    
    For the purpose of calculating diluted earnings per share, net income (loss) available to
common stockholders was reduced to adjust for the effects of options issued by Alons
subsidiaries. The adjustment to net income (loss) available to common stockholders for
options issued for the calculation of diluted earnings per share for December 31, 2009 was
anti-dilutive and therefore excluded from the calculation, for 2008 and 2007 the adjustment
was $1,449, and $2,391, respectively. Additionally, net income (loss) available to common
stockholders for the year ended December 31, 2008 was adjusted $3,991 for preferred stock
dividends that would no longer be paid if the preferred stock was converted to shares of
common stock. On December 31, 2009, the preferred stock was converted to shares of common
stock (Note 17). (20) Stock Based Compensation
  (a) 2005 Incentive Compensation Plan (share value in dollars)
  Restricted Stock
  Weighted AverageNonvested Shares
    
    Shares
    
    
    Grant Date Fair ValuesNonvested at January 1, 2009
    
    
    7,662
    
    
    $
    19.58Granted
    
    
    5,841
    
    
    
    12.84Vested
    
    
    (3,277
    )
    
    
    22.89Forfeited
    
    
    
    
    
    
    Nonvested at December 31, 2009
    
    
    10,226
    
    
    $
    14.67
 F-40




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Stock Appreciation Rights.
       (b) 2000 Incentive Stock Compensation Plan
  F-41




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Alon Assets
    
    
    Alon OperatingWeighted
    
    
    
    
    
    
    WeightedNumber of
    
    
    Average
    
    
    Number of
    
    
    AverageOptions
    
    
    Exercise
    
    
    Options
    
    
    ExerciseOutstanding
    
    
    Price
    
    
    Outstanding
    
    
    PriceOutstanding at December 31, 2007
    
    
    5,216
    
    
    $
    100
    
    
    
    1,959
    
    
    $
    100Granted
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Exercised
    
    
    (2,423
    )
    
    
    100
    
    
    
    (910
    )
    
    
    100Forfeited and expired
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Outstanding at December 31, 2008
    
    
    2,793
    
    
    $
    100
    
    
    
    1,049
    
    
    $
    100Granted
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Exercised
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Forfeited and expired
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Outstanding at December 31, 2009
    
    
    2,793
    
    
    $
    100
    
    
    
    1,049
    
    
    $
    100
  (21) Commitments and Contingencies
 (a) Leases
  Year ending December 31:2010
    
    $
    35,9502011
    
    
    30,2792012
    
    
    25,7932013
    
    
    14,3402014
    
    
    11,3672015 and thereafter
    
    
    65,025Total
    
    $
    182,754
  (b) Other Commitments
   F-42




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
     (c) Environmental
    F-43




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
    (22) Quarterly Information (unaudited)
  QuartersFirst
    
    Second
    
    Third
    
    Fourth
    
    Full Year2009Net sales
    
    $
    722,180
    
    
    $
    1,106,398
    
    
    $
    1,253,113
    
    
    $
    834,041
    
    
    $
    3,915,732Operating income (loss)
    
    
    59,581
    
    
    
    (10,007
    )
    
    
    (34,343
    )
    
    
    (96,067
    )
    
    
    (80,836
    )Net income (loss) available to
common stockholders
    
    
    17,351
    
    
    
    (15,340
    )
    
    
    (26,558
    )
    
    
    (90,609
    )
    
    
    (115,156
    )Earnings (loss) per share, basic
    
    $
    0.37
    
    
    $
    (0.33
    )
    
    $
    (0.57
    )
    
    $
    (1.93
    )
    
    $
    (2.46
    )Weighted average shares outstanding
    
    
    46,806
    
    
    
    46,809
    
    
    
    46,810
    
    
    
    46,890
    
    
    
    46,8292008Net sales
    
    $
    1,020,763
    
    
    $
    1,244,671
    
    
    $
    1,905,106
    
    
    $
    986,166
    
    
    $
    5,156,706Operating income (loss)
    
    
    (47,273
    )
    
    
    40,573
    
    
    
    92,505
    
    
    
    137,672
    
    
    
    223,477Net income (loss) available to
common stockholders
    
    
    (33,578
    )
    
    
    18,227
    
    
    
    37,297
    
    
    
    60,937
    
    
    
    82,883Earnings (loss) per share, basic
    
    $
    (0.72
    )
    
    $
    0.39
    
    
    $
    0.80
    
    
    $
    1.30
    
    
    $
    1.77Weighted average shares outstanding
    
    
    46,782
    
    
    
    46,782
    
    
    
    46,786
    
    
    
    46,800
    
    
    
    46,788
 (23) Subsequent Events
 Bakersfield Refinery
   F-44




---



##### Table of Contents



ALON USA ENERGY, INC. AND SUBSIDIARIES
NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
(dollars in thousands except as noted)
  Related Party Transaction
  F-45




---



##### Table of Contents



SIGNATURES
  March 16, 2010
    
    By:
    
    /s/ Jeff D. MorrisJeff D. MorrisChief Executive Officer
  March 16, 2010
    
    By:
    
    /s/ David WiessmanDavid WiessmanExecutive Chairman of the BoardMarch 16, 2010
    
    By:
    
    /s/ Jeff D. MorrisJeff D. MorrisChief Executive Officer and DirectorMarch 16, 2010
    
    By:
    
    /s/ Shai EvenShai EvenSenior Vice President and Chief Financial OfficerMarch 16, 2010
    
    By:
    
    /s/ Ron W. HaddockRon W. HaddockDirectorMarch 16, 2010
    
    By:
    
    /s/ Itzhak BaderItzhak BaderDirectorMarch 16, 2010
    
    By:
    
    /s/ Avraham Baiga ShochatAvraham Baiga ShochatDirectorMarch 16, 2010
    
    By:
    
    /s/ Yeshayahu PeryYeshayahu PeryDirectorMarch 16, 2010
    
    By:
    
    /s/ Zalman SegalZalman SegalDirectorMarch 16, 2010
    
    By:
    
    /s/ Boaz BiranBoaz BiranDirectorMarch 16, 2010
    
    By:
    
    /s/ Avinadav GrinshponAvinadav GrinshponDirectorMarch 16, 2010
    
    By:
    
    /s/ Shlomo EvenShlomo EvenDirector




---



##### Table of Contents



Exhibit Index
 Exhibit No.
    
    Description of Exhibit3.1
    
    Amended and Restated Certificate of Incorporation of Alon USA Energy, Inc. (incorporated by
reference to Exhibit 3.1 to Form S-1/A, filed by the Company on July 7, 2005, SEC File No.
333-124797).3.2
    
    Amended and Restated Bylaws of Alon USA Energy, Inc. (incorporated by reference to Exhibit
3.2 to Form S-1/A, filed by the Company on July 14, 2005, SEC File No. 333-124797).4.1
    
    Specimen Common Stock Certificate (incorporated by reference to Exhibit 4.1 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).4.2
    
    Indenture, dated as of October 22, 2009, by and among Alon Refining Krotz Springs, Inc. and
Wilmington Trust FSB, as Trustee (incorporated by reference to Exhibit 4.1 to Form 8-K,
filed by the Company on October 23, 2009, SEC File No. 001-32567).10.1
    
    Trademark License Agreement, dated as of July 31, 2000, among Finamark, Inc., Atofina
Petrochemicals, Inc. and SWBU, L.P. (incorporated by reference to Exhibit 10.3 to Form S-1,
filed by the Company on May 11, 2005, SEC File No. 333-124797).10.2
    
    First Amendment to Trademark License Agreement, dated as of April 11, 2001, among Finamark,
Inc., Atofina Petrochemicals, Inc. and SWBU, L.P. (incorporated by reference to Exhibit 10.4
to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.3
    
    Pipeline Lease Agreement, dated as of December 12, 2007, between Plains Pipeline, L.P. and
Alon USA, L.P. (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company
on February 2, 2008, SEC File No. 001-32567).10.4
    
    Pipeline Lease Agreement, dated as of February 21, 1997, between Navajo Pipeline Company and
American Petrofina Pipe Line Company (incorporated by reference to Exhibit 10.6 to Form S-1,
filed by the Company on May 11, 2005, SEC File No. 333-124797).10.5
    
    Amendment and Supplement to Pipeline Lease Agreement, dated as of August 31, 2007, by and
between HEP Pipeline Assets, Limited Partnership and Alon USA, LP (incorporated by reference
to Exhibit 10.1 to Form 10-Q, filed by the Company on November 8, 2007).10.6
    
    Contribution Agreement, dated as of January 25, 2005, among Holly Energy Partners, L.P.,
Holly Energy Partners  Operating, L.P., T & R Assets, Inc., Fin-Tex Pipe Line Company,
Alon USA Refining, Inc., Alon Pipeline Assets, LLC, Alon Pipeline Logistics, LLC, Alon USA,
Inc. and Alon USA, LP (incorporated by reference to Exhibit 10.7 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.7
    
    Pipelines and Terminals Agreement, dated as of February 28, 2005, between Alon USA, LP and
Holly Energy Partners, L.P. (incorporated by reference to Exhibit 10.8 to Form S-1, filed by
the Company on May 11, 2005, SEC File No. 333-124797).10.8
    
    Pipeline Lease Agreement, dated as of December 12, 2007, between Plains Pipeline, L.P. and
Alon USA, LP (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on
February 5, 2008, SEC File No. 001-32567).




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.9
    
    Liquor License Purchase Agreement, dated as of May 12, 2003, between Southwest Convenience
Stores, LLC and SCS Beverage, Inc. (incorporated by reference to Exhibit 10.34 to Form
S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.10
    
    Premises Lease, dated as of May 12, 2003, between Southwest Convenience Stores, LLC and SCS
Beverage, Inc. (incorporated by reference to Exhibit 10.35 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.11
    
    Registration Rights Agreement, dated as of July 6, 2005, between Alon USA Energy, Inc. and
Alon Israel Oil Company, Ltd. (incorporated by reference to Exhibit 10.22 to Form S-1/A,
filed by the Company on July 7, 2005, SEC File No. 333-124797).10.12
    
    Registration Rights Agreement, dated October 22, 2009, between Alon Refining Krotz Springs,
Inc. and Jefferies & Company, Inc. (incorporated by reference to Exhibit 10.2 to Form 8-K,
filed by the Company on October 23, 2009, SEC File No. 001-32567).10.13
    
    Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA, LP, EOC
Acquisition, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.2 to Form 8-K, filed by the Company on June 26, 2006, SEC File
No. 001-32567).10.14
    
    First Amendment to Amended Revolving Credit Agreement, dated as of August 4, 2006, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA, LP, EOC
Acquisition, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.25 to Form 10-K, filed by the Company on March 15, 2007 SEC File
No. 001-32567).10.15
    
    Waiver, Consent, Partial Release and Second Amendment, dated as of February 28, 2007, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, Alon USA, LP, Edgington Oil
Company, LLC, Israel Discount Bank of New York, Bank Leumi USA and certain other guarantor
companies and financial institutions from time to time named therein (incorporated by
reference to Exhibit 10.2 to Form 8-K, filed by the Company on March 5, 2007, SEC File No.
001-32567).10.16
    
    Third Amendment to Amended Revolving Credit Agreement, dated as of June 29, 2007, to the
Amended Revolving Credit Agreement, dated as of June 22, 2006, among Alon USA Energy, Inc.,
Alon USA, LP, the guarantor companies and financial institutions named therein, Israel
Discount Bank of New York and Bank Leumi USA (incorporated by reference to Exhibit 10.1 to
Form 8-K, filed by the Company on July 20, 2007, SEC File No. 001-32567).10.17
    
    Waiver, Consent, Partial Release and Fourth Amendment, dated as of July 2, 2008, by and
among Alon USA, LP, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.4 to Form 8-K, filed by the Company on July 10, 2008, SEC File
No. 001-32567).10.18
    
    Fifth Amendment to Amended Revolving Credit Agreement, dated as of July 31, 2009, by and
among Alon USA, LP, Israel Discount Bank of New York, Bank Leumi USA and certain other
guarantor companies and financial institutions from time to time named therein (incorporated
by reference to Exhibit 10.3 to Form 10-Q, filed by the Company on August 6, 2009, SEC File
No. 001-32567).10.19
    
    Credit Agreement, dated as of July 30, 2008, among Alon USA Energy, Inc., the financial
institutions from time to time party thereto, Israel Discount Bank and Bank Leumi USA
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on August 1,
2008, SEC File No. 001-32567).10.20
    
    Amended and Restated Credit Agreement, dated as of June 29, 2007, among Southwest
Convenience Stores, LLC, the lenders party thereto and Wachovia Bank, National Association
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on July 2,
2007, SEC File No. 001-32567).10.21
    
    Credit Agreement, dated as of June 22, 2006, among Alon USA Energy, Inc., the lenders party
thereto and Credit Suisse (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by
the Company on June 26, 2006, SEC File No. 001-32567).




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.22
    
    Amendment No. 1 to the Credit Agreement, dated as of February 28, 2007, by and among Alon
USA Energy, Inc., the lenders party thereto and Credit Suisse (incorporated by reference to
Exhibit 10.3 to Form 8-K, filed by the Company on March 5, 2007, SEC File No. 001-32567).10.23
    
    Second Amended and Restated Credit Agreement, dated as of February 28, 2007, among Paramount
Petroleum Corporation, Bank of America, N.A. and certain other guarantor companies and
financial institutions from time to time named therein (incorporated by reference to Exhibit
10.1 to Form 8-K, filed by the Company on March 5, 2007, SEC File No. 001-32567).10.24
    
    First Amendment to Second Amended and Restated Credit Agreement, dated as of March 30, 2007,
among Paramount Petroleum Corporation, Bank of America, N.A. and certain other guarantor
companies and financial institutions from time to time named therein (incorporated by
reference to Exhibit 10.37 to Form 10-K, filed by the Company on March 11, 2008, SEC File
No. 001-32567).10.25
    
    Term Loan Agreement, dated as of July 3, 2008, by and among Alon Refining Louisiana, Inc.,
Alon Refining Krotz Springs, Inc., the lenders party thereto and Credit Suisse, as
administrative agent and collateral agent (incorporated by reference to Exhibit 10.2 to Form
8-K, filed by the Company on July 10, 2008, SEC File No. 001-32567).10.26
    
    First Amendment Agreement, dated as of April 9, 2009, by and among Alon Refining Louisiana,
Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto and Wells Fargo Bank, National
Association, as successor to Credit Suisse, Cayman Islands Branch, as agent (incorporated by
reference to Exhibit 10.1 to Form 10-Q, filed by the Company on August 6, 2009, SEC File No.
001-32567).10.27
    
    Loan and Security Agreement, dated as of July 3, 2008, by and among Alon Refining Louisiana,
Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto and Bank of America,
N.A., as administrative agent (incorporated by reference to Exhibit 10.3 to Form 8-K, filed
by the Company on July 10, 2008, SEC File No. 001-32567).10.28
    
    First Amendment to Loan and Security Agreement, dated as of December 18, 2008, by and among
Alon Refining Louisiana, Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto
and Bank of America, N.A. (incorporated by reference to Exhibit 10.28 to Form 10-K, filed by
the Company on April 10, 2009, SEC File No. 001-32567).10.29
    
    Second Amendment to Loan and Security Agreement, dated as of April 9, 2009, by and among
Alon Refining Louisiana, Inc., Alon Refining Krotz Springs, Inc., the lenders party thereto and Bank
of America, N.A., as agent (incorporated by reference to Exhibit 10.2 to Form 8-K, filed by
the Company on April 27, 2009, SEC File No. 001-32567).10.30
    
    Amended and Restated Loan and Security Agreement, dated as of October 22, 2009 (as amended,
supplemented or otherwise modified from time to time), among Alon Refining Louisiana, Inc.,
Alon Refining Krotz Springs, Inc., each other party joined as a borrower thereunder from
time to time, the Lenders party thereto, and Bank of America, N.A., as Agent (incorporated
by reference to Exhibit 10.1 to Form 8-K, filed by the Company on October 23, 2009, SEC File
No. 001-32567).10.31
    
    Purchase Agreement dated October 13, 2009, between Alon Refining Krotz Springs, Inc. and
Jefferies & Co. (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company
on October 19, 2009, SEC File No. 001-32567).10.32
    
    Management and Consulting Agreement, dated as of August 1, 2003, among Alon USA, Inc., Alon
Israel Oil Company, Ltd. and Alon USA Energy, Inc. (incorporated by reference to Exhibit
10.21 to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.33
    
    Amendment, dated as of June 17, 2005, to the Management and Consulting Agreement, dated as
of August 1, 2003, among Alon USA, Inc., Alon Israel Oil Company, Ltd. and Alon USA Energy,
Inc. (incorporated by reference to Exhibit 10.21.1 to Form S-1/A, filed by the Company on
June 17, 2005, SEC File No. 333-124797).10.34*
    
    Executive Employment Agreement, dated as of July 31, 2000, between Jeff D. Morris and Alon
USA GP, Inc., as amended by the Amendment to Executive/Management Employment Agreement,
dated May 1, 2005 (incorporated by reference to Exhibit 10.23 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.35*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon USA GP, LLC (incorporated by reference to Exhibit 10.9 to Form 10-Q,
filed by the Company on November 7, 2008, SEC File No. 001-32567).10.36*
    
    Executive Employment Agreement, dated as of July 31, 2000, between Claire A. Hart and Alon
USA GP, Inc., as amended by the Amendment to Executive/Management Employment Agreement,
dated May 1, 2005 (incorporated by reference to Exhibit 10.24 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.37*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Claire A. Hart and Alon USA GP, LLC (incorporated by reference to Exhibit 10.10 to Form
10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.38*
    
    Executive Employment Agreement, dated as of February 5, 2001, between Joseph A. Concienne,
III and Alon USA GP, Inc., as amended by the Amendment to Executive/Management Employment
Agreement, dated May 1, 2005 (incorporated by reference to Exhibit 10.25 to Form S-1, filed
by the Company on May 11, 2005, SEC File No. 333-124797).10.39*
    
    Second Amendment to Executive Employment Agreement, dated as of November 4, 2008, between
Joseph A. Concienne, III and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.11
to Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.40*
    
    Amended and Restated Management Employment Agreement, dated as of August 9, 2006, between
Harlin R. Dean and Alon USA GP, LLC (incorporated by reference to Exhibit 10.1 to Form 8-K,
filed by the Company on August 10, 2006, SEC File No. 001-32567).10.41*
    
    Amendment to Amended and Restated Management Employment Agreement, dated as of November 4,
2008, between Harlin R. Dean and Alon USA GP, LLC (incorporated by reference to Exhibit
10.12 to Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.42*
    
    Management Employment Agreement, dated as of September 1, 2000, between Yosef Israel and
Alon USA GP, LLC (incorporated by reference to Exhibit 10.33 to Form 10-K, filed by the
Company on March 15, 2006, SEC File No. 001-32567).10.43*
    
    Amendment to Executive/Management Employment Agreement, dated as of May 1, 2005 between
Yosef Israel and Alon USA GP, LLC (incorporated by reference to Exhibit 10.34 to Form 10-K,
filed by the Company on March 15, 2006, SEC File No. 001-32567).10.44*
    
    Second Amendment to Executive/Management Employment Agreement, dated as of November 4, 2008,
between Yosef Israel and Alon USA GP, LLC (incorporated by reference to Exhibit 10.13 to
Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.45*
    
    Executive Employment Agreement, dated as of August 1, 2003, between Shai Even and Alon USA
GP, LLC (incorporated by reference to Exhibit 10.49 to Form 10-K, filed by the Company on
March 15, 2007, SEC File No. 001-32567).10.46*
    
    Amendment to Executive Employment Agreement, dated as of November 4, 2008, between Shai Even
and Alon USA GP, LLC. (incorporated by reference to Exhibit 10.14 to Form 10-Q, filed by the
Company on November 7, 2008, SEC File No. 001-32567).10.47*
    
    Agreement of Principles of Employment, dated as of July 6, 2005, between David Wiessman and
Alon USA Energy, Inc. (incorporated by reference to Exhibit 10.50 to Form S-1/A, filed by
the Company on July 7, 2005, SEC File No. 333-124797).10.48*
    
    Management Employment Agreement, dated as of October 30, 2008, between Michael Oster and
Alon USA GP, LLC (incorporated by reference to Exhibit 10.71 to Form 10-K, filed by the
Company on April 10, 2009, SEC File No. 001-32567).10.49*
    
    Annual Cash Bonus Plan (incorporated by reference to Exhibit 10.27 to Form S-1, filed by the
Company on May 11, 2005, SEC File No. 333-124797).10.50*
    
    Description of 10% Bonus Plan (incorporated by reference to Exhibit 10.28 to Form S-1, filed
by the Company on May 11, 2005, SEC File No. 333-124797).10.51*
    
    Description of Annual Bonus Plans (incorporated by reference to Exhibit 10.2 to Form 10-Q,
filed by the Company on May 6, 2008, SEC File No. 001-32567).




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.52*
    
    Change of Control Incentive Bonus Program (incorporated by reference to Exhibit 10.29 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.53*
    
    Description of Director Compensation (incorporated by reference to Exhibit 10.30 to Form
S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.54*
    
    Form of Director Indemnification Agreement (incorporated by reference to Exhibit 10.31 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.55*
    
    Form of Officer Indemnification Agreement (incorporated by reference to Exhibit 10.32 to
Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.56*
    
    Form of Director and Officer Indemnification Agreement (incorporated by reference to Exhibit
10.33 to Form S-1, filed by the Company on May 11, 2005, SEC File No. 333-124797).10.57*
    
    Alon Assets, Inc. 2000 Stock Option Plan (incorporated by reference to Exhibit 10.36 to Form
S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.58*
    
    Alon USA Operating, Inc. 2000 Stock Option Plan (incorporated by reference to Exhibit 10.37
to Form S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).10.59*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and
Jeff D. Morris, as amended by the Amendment to the Incentive Stock Option Agreement, dated
June 30, 2002 (incorporated by reference to Exhibit 10.38 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.60*
    
    Second Amendment to Incentive Stock Option Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon Assets, Inc. (incorporated by reference to Exhibit 10.15 to Form
10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.61
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and Jeff D.
Morris, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.39 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.62*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon USA Operating,
Inc. and Jeff D. Morris, as amended by the Amendment to the Incentive Stock Option
Agreement, dated June 30, 2002 (incorporated by reference to Exhibit 10.40 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.63*
    
    Second Amendment to Incentive Stock Option Agreement, dated as of November 4, 2008, between
Jeff D. Morris and Alon USA Operating, Inc. (incorporated by reference to Exhibit 10.16 to
Form 10-Q, filed by the Company on November 7, 2008, SEC File No. 001-32567).10.64
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon USA Operating, Inc. and Jeff
D. Morris, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.41 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.65*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and
Claire A. Hart, as amended by the Amendment to the Incentive Stock Option Agreement, dated
June 30, 2002 and July 25, 2002 (incorporated by reference to Exhibit 10.42 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.66
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon Assets, Inc. and Claire A.
Hart, as amended by the Amendment to the Shareholder Agreement, dated June 30, 2002
(incorporated by reference to Exhibit 10.43 to Form S-1/A, filed by the Company on June 17,
2005, SEC File No. 333-124797).10.67*
    
    Incentive Stock Option Agreement, dated as of July 31, 2000, between Alon USA Operating,
Inc. and Claire A. Hart, as amended by the Amendment to the Incentive Stock Option
Agreement, dated June 30, 2002 and July 25, 2002 (incorporated by reference to Exhibit 10.44
to Form S-1/A, filed by the Company on June 17, 2005, SEC File No. 333-124797).




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.68
    
    Shareholder Agreement, dated as of July 31, 2000, between Alon USA Operating, Inc. and
Claire A. Hart, as amended by the Amendment to the Shareholder Agreement, dated June 30,
2002 (incorporated by reference to Exhibit 10.45 to Form S-1/A, filed by the Company on June
17, 2005, SEC File No. 333-124797).10.69*
    
    Incentive Stock Option Agreement, dated as of February 5, 2001, between Alon Assets, Inc.
and Joseph A. Concienne, III, as amended by the Amendment to the Incentive Stock Option
Agreement, dated July 25, 2002 (incorporated by reference to Exhibit 10.46 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.70
    
    Shareholder Agreement, dated as of February 5, 2001, between Alon Assets, Inc. and Joseph A.
Concienne, III (incorporated by reference to Exhibit 10.47 to Form S-1/A, filed by the
Company on June 17, 2005, SEC File No. 333-124797).10.71*
    
    Incentive Stock Option Agreement, dated as of February 5, 2001, between Alon USA Operating,
Inc. and Joseph A. Concienne, III, as amended by the Amendment to the Incentive Stock Option
Agreement, dated July 25, 2002 (incorporated by reference to Exhibit 10.48 to Form S-1/A,
filed by the Company on June 17, 2005, SEC File No. 333-124797).10.72
    
    Shareholder Agreement, dated as of February 5, 2001, between Alon USA Operating, Inc. and
Joseph A. Concienne, III (incorporated by reference to Exhibit 10.49 to Form S-1/A, filed by
the Company on June 17, 2005, SEC File No. 333-124797).10.73
    
    Agreement, dated as of July 6, 2005, among Alon USA Energy, Inc., Alon USA, Inc., Alon USA
Capital, Inc., Alon USA Operating, Inc., Alon Assets, Inc., Jeff D. Morris, Claire A. Hart
and Joseph A. Concienne, III (incorporated by reference to Exhibit 10.52 to Form S-1/A,
filed by the Company on July 7, 2005, SEC File No. 333-124797).10.74*
    
    Alon USA Energy, Inc. 2005 Incentive Compensation Plan, as amended on November 7, 2005
(incorporated by reference to Exhibit 10.2 to Form 8-K, filed by the Company on November 8,
2005, SEC File No. 001-32567).10.75*
    
    Form of Restricted Stock Award Agreement relating to Director Grants pursuant to Section 12
of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by reference to
Exhibit 10.1 to Form 8-K, filed by the Company on August 5, 2005, SEC File No. 001-32567).10.76*
    
    Form of Restricted Stock Award Agreement relating to Participant Grants pursuant to Section
8 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by reference
to Exhibit 10.1 to Form 8-K, filed by the Company on August 23, 2005, SEC File No.
001-32567).10.77*
    
    Form II of Restricted Stock Award Agreement relating to Participant Grants pursuant to
Section 8 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.3 to Form 8-K, filed by the Company on November 8, 2005, SEC File
No. 001-32567).10.78*
    
    Form of Appreciation Rights Award Agreement relating to Participant Grants pursuant to
Section 7 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.1 to Form 8-K, filed by the Company on March 12, 2007, SEC File No.
001-32567).10.79*
    
    Form of Amendment to Appreciation Rights Award Agreement relating to Participant Grants
pursuant to Section 7 of the Alon USA Energy, Inc. 2005 Incentive Compensation Plan
(incorporated by reference to Exhibit 10.2 to Form 8-K, filed by the Company on January 27,
2010, SEC File No. 001-32567).10.80*
    
    Form II of Appreciation Rights Award Agreement relating to Participant Grants pursuant to
Section 7 of the Alon USA Energy, inc. 2005 Incentive Compensation Plan (incorporated by
reference to Exhibit 10.1 to Form 8-K, filed by the Company on January 27, 2010, SEC File
No. 001-32567).10.81
    
    Purchase and Sale Agreements, dated as of February 13, 2006, between Alon Petroleum Pipe
Line, LP and Sunoco Pipelines, LP, (incorporated by reference to Exhibit 10.1 to Form 8-K,
filed by the Company on February 13, 2006, SEC File No. 001-32567).10.82
    
    Stock Purchase Agreement, dated as of April 28, 2006, among Alon USA Energy, Inc., The Craig
C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The Jerrel C. Barto and
Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy, III and Mark R. Milano
(incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on May 2, 2006,
SEC File No. 001-32567).




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit10.83
    
    First Amendment to Stock Purchase Agreement, dated as of June 30, 2006, among Alon USA
Energy, Inc., The Craig C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The
Jerrel C. Barto and Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy III
and Mark R. Milano (incorporated by reference to Exhibit 10.1 to Form 10-Q, filed by the
Company on November 14, 2006, SEC File No. 001-32567).10.84
    
    Second Amendment to Stock Purchase Agreement, dated as of July 31, 2006, among Alon USA
Energy, Inc., The Craig C. Barto and Gisele M. Barto Living Trust, Dated April 5, 1991, The
Jerrel C. Barto and Janice D. Barto Living Trust, Dated March 18, 1991, W. Scott Lovejoy III
and Mark R. Milano (incorporated by reference to Exhibit 10.2 to Form 10-Q, filed by the
Company on November 14, 2006, SEC File No. 001-32567).10.85
    
    Agreement and Plan of Merger, dated as of April 28, 2006, among Alon USA Energy, Inc., Apex
Oil Company, Inc., Edgington Oil Company, and EOC Acquisition, LLC (incorporated by
reference to Exhibit 10.2 to Form 8-K, filed by the Company on May 2, 2006, SEC File No.
001-32567).10.86
    
    Agreement and Plan of Merger, dated March 2, 2007, by and among Alon USA Energy, Inc., Alon
USA Interests, LLC, ALOSKI, LLC, Skinnys, Inc. and the Davis Shareholders (as defined
therein) (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the Company on
March 6, 2007, SEC File No. 001-32567).10.87
    
    Stock Purchase Agreement, dated May 7, 2008, between Valero Refining and Marketing Company
and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.1 to Form
8-K, filed by the Company on May 13, 2008, SEC File No. 001-32567).10.88
    
    First Amendment to Stock Purchase Agreement, dated as of July 3, 2008, by and among Valero
Refining and Marketing Company, Alon Refining Krotz Springs, Inc. and Valero Refining
Company-Louisiana (incorporated by reference to Exhibit 10.1 to Form 8-K, filed by the
Company on July 10, 2008, SEC File No. 001-32567).10.89
    
    Series A Preferred Stock Purchase Agreement, dated as of July 3, 2008, by and between Alon
Refining Louisiana, Inc. and Alon Israel Oil Company, Ltd. (incorporated by reference to
Exhibit 10.5 to Form 8-K, filed by the Company on July 10, 2008, SEC File No. 001-32567).10.90
    
    Stockholders Agreement, dated as of July 3, 2008, by and among Alon USA Energy, Inc., Alon
Refining Louisiana, Inc., Alon Louisiana Holdings, Inc. and Alon Israel Oil Company, Ltd.
(incorporated by reference to Exhibit 10.6 to Form 8-K, filed by the Company on July 10,
2008, SEC File No. 001-32567).10.91
    
    Amended and Restated Stockholders Agreement dated as of March 31, 2009, by and among Alon
USA Energy, Inc., Alon Refining Louisiana, Inc., Alon Louisiana Holdings, Inc. and Alon
Israel Oil Company, Ltd. (incorporated by reference to Exhibit 10.88 to Form 10-K, filed by
the Company on April 10, 2009, SEC File No. 001-32567).10.92
    
    First Amendment to Amended and Restated Stockholders Agreement dated as of December 31,
2009, by and among Alon USA Energy, Inc., Alon Refining Louisiana, Inc., Alon Louisiana
Holdings, Inc. and Alon Israel Oil Company, Ltd. (incorporated by reference to Exhibit 10.1
to Form 8-K, filed by the Company on January 5, 2010, SEC File No. 001-32567).10.93
    
    Offtake Agreement, dated as of July 3, 2008, by and between Valero Marketing and Supply
Company and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.9 to
Form 10-Q, filed by the Company on August 8, 2008, SEC File No. 001-32567).10.94
    
    Earnout Agreement, dated as of July 3, 2008, by and between Valero Refining and Marketing
Company and Alon Refining Krotz Springs, Inc. (incorporated by reference to Exhibit 10.10 to
Form 10-Q, filed by the Company on August 8, 2008, SEC File No. 001-32567).10.95
    
    First Amendment to Earnout Agreement, dated as of August 27, 2009, by and between Valero
Refining and Marketing Company and Alon Refining Krotz Springs, Inc. (incorporated by
reference to Exhibit 10.1 to Form 10-Q, filed by the Company on November 6, 2009, SEC File
No. 001-32567).10.96
    
    Revolving Credit Line Agreement dated March 9, 2010 by and between the Company and Israel Discount Bank of New York.10.97
    
    Credit Agreement dated as of March 15, 2010 (as amended, supplemented or otherwise
modified from time to time), among the Company, each other party joined as a
borrower thereunder from time to time, the Lenders party thereto, and Bank Hapoalim B.M., as Administrative Agent.




---



##### Table of Contents



Exhibit No.
    
    Description of Exhibit12.1
    
    Statement Regarding Computation of
Ratio of Earnings to Fixed Charges.21.1
    
    Subsidiaries of Alon USA Energy, Inc.23.1
    
    Consent of KPMG LLP.31.1
    
    Certifications of Chief Executive Officer pursuant to §302 of the Sarbanes-Oxley Act of 2002.31.2
    
    Certifications of Chief Financial Officer pursuant to §302 of the Sarbanes-Oxley Act of 2002.32.1
    
    Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C.
§1350, as adopted pursuant to §906 of the Sarbanes-Oxley Act of 2002.
 
 *
    
    Identifies management contracts and compensatory plans or arrangements.
    
    Filed under confidential treatment request.