Exhibit 10.28
FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT
     This FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT (this “Amendment”),
dated as of December 18, 2008, among ALON REFINING KROTZ SPRINGS, INC. (the
“Company”), as a Borrower, ALON REFINING LOUISIANA, INC. (“Holdings”), and BANK
OF AMERICA, N.A. (“Bank of America”), as Agent and a Lender. Unless otherwise
defined in this Amendment, all initially capitalized terms and phrases wherever
used in this Amendment shall have the respective meanings given to them in the
Loan Agreement (as defined below), as amended hereby.
RECITALS:
     A. WHEREAS, the Company, each other party joined thereto as a Borrower from
time to time, Holdings, the Lenders party thereto from time to time, and the
Agent executed that certain Loan and Security Agreement dated as of July 3, 2008
(as amended, supplemented, or otherwise modified from time to time, the “Loan
Agreement”), pursuant to which the Lenders have agreed to make available to the
Borrowers a revolving line of credit; and
     B. WHEREAS, the Company, Holdings, the Lenders, and the Agent desire that
the Loan Agreement be amended in certain respects in accordance with the terms
of this Amendment.
     NOW, THEREFORE, in consideration of the premises and for other valuable
consideration, the receipt and sufficiency of which are hereby acknowledged, the
parties hereto hereby agree as follows:
     1. Recitals. The foregoing Recitals are accurate and are incorporated
herein and made a part hereof for all purposes.
     2. Amendments to Loan Agreement. Subject to the terms and conditions set
forth herein, as of the First Amendment Effective Date (as defined below), the
Loan Agreement is hereby amended as follows:
               (a) Amendment of Certain Definitions Appearing in Section 1.1 of
the Loan Agreement. The following definitions appearing in Section 1.1 of the
Loan Agreement are hereby amended and restated in their entirety as follows:
“ Applicable Margin: with respect to any Type of Loan or the Unused Line Fee,
the margin set forth below, as determined by the Fixed Charge Coverage Ratio for
the last Four Quarter Period:

                                                                      LIBOR  
Standby   Documentary                 Base Rate   Revolver   Letters of  
Letters of   Unused Level   Ratio   Loans   Loans   Credit   Credit   Line Fee  
I    
Greater than 1.40 to 1.00
    1.25 %     2.75 %     2.75 %     2.25 %     0.250 % II  
Less than or equal to 1.40 to 1.00 but greater than 1.25 to 1.00
    1.50 %     3.00 %     3.00 %     2.50 %     0.250 % III  
Less than or equal to 1.25 to 1.00 but greater than 1.00 to 1.00
    1.75 %     3.25 %     3.25 %     2.75 %     0.375 % IV  
Less than or equal to 1.00 to 1.00
    2.00 %     3.50 %     3.50 %     3.00 %     0.500 %

Until the date of receipt by the Agent of the quarterly financial statements
delivered for the Fiscal

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Quarter ending December 31, 2008, the Applicable Margins shall be determined as
if Level II were applicable. Thereafter, the margins shall be subject to
increase or decrease upon receipt by Agent pursuant to Section 10.1.4 of the
financial statements and corresponding Compliance Certificate for the last
Fiscal Quarter, which change shall be effective on the first day of the calendar
month following receipt. If, by the first day of a month, any financial
statements and Compliance Certificate due in the preceding month have not been
received, then the margins shall be determined as if Level IV were applicable,
from such day until the first day of the calendar month following actual
receipt.”
“ Borrowing Base: on any date of determination, an amount equal to the lesser
of:
     (a) the aggregate amount of Revolver Commitments, minus the LC Obligations;
and
     (b) the difference of:
(i) the sum of
     (A) (1) 90% of the Net Amount of Eligible Major Accounts and (2) 85% of the
Net Amount of Eligible Other Accounts; provided, that each such percentage shall
be reduced by .1% for each .1 percentage point that the Dilution Percent exceeds
2.5%, plus
     (B) 85% of the sum of (1) Eligible Petroleum Inventory and (2) Eligible
Petroleum Inventory in Transit; plus
     (C) 80% of the DOE Contract Value, such advance rate to be reduced by 5%
per week beginning January 2, 2009, with such a reduction continuing on each
Friday thereafter until February 1, 2009. Upon the earlier to occur of
(i) February 1, 2009, and (ii) termination or modification of the Crack Spread
Hedge Agreement resulting in the Company or Holdings receiving not less than
$25,000,000 or any Obligor receiving subordinated debt or a capital contribution
of not less than $25,000,000, the advance rate under this subsection (b)(i)(C)
shall be reduced to 0.0%; plus
     (D) 100% of Eligible Cash, plus
     (E) 95% of Eligible Investments, plus
     (F) 100% of the amount available to be drawn by the Agent on the Supporting
Letter of Credit; plus
     (G) 100% of Paid but Unexpired Letters of Credit; minus
(ii) the Availability Reserve;
provided, that no Accounts or Petroleum Product acquired in an Acquisition
consummated by any Obligor after the Closing Date shall be included in any
calculation of the Borrowing Base until completion of all field exams,
appraisals, audits and other evaluation of Collateral in a manner and with
results acceptable to Agent.”

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          (b) Addition of Certain Definitions to Section 1.1 of the Loan
Agreement. The following definitions are hereby added to Section 1.1 of the Loan
Agreement in proper alphabetical order as follows:
“ DOE Contract Value: On any date of determination, the decrease, if any, in the
cost of the exchange oil plus premium barrels, determined on a Marked-to-Market
Basis as set forth in Schedule 1.2 of the Loan Agreement, under those certain
Department of Energy Oil Exchange Agreements (DE-FE 93008, DE-FE 92300, DE-FE
93003, DE-FE 93006 and DE-FE 93010) (collectively “DOE Contracts”) between the
date of each such DOE Contract and the date of determination.”
          (c) Reduction of Revolver Commitment. Schedule 1.1 of the Loan
Agreement is hereby modified by deleting “$400,000,000” and replacing it with
“$300,000,000”; provided that if the Revolver Commitment is fully syndicated
(with Bank of America’s hold, in its capacity as a Lender, at no more than
$50,000,000), the Revolver Commitment may be increased above $300,000,000 to a
maximum of $400,000,000 if Agent receives commitments from new or existing
Lenders to increase the Revolver Commitment. All Lenders must be reasonably
acceptable to Agent.
          (d) Amendment of Section 8.1 of the Loan Agreement. Section 8.1 of the
Loan Agreement is hereby amended and restated in its entirety as follows:
“ 8.1 Borrowing Base Certificates. The Borrowers shall deliver to the Agent
(a) if no Low Availability Period is in effect, then on or before the 15th day
of each month, a Borrowing Base Certificate as of the end of the previous month,
or (b) if a Low Availability Period is in effect, then on each Tuesday of each
week for the period ending Friday of the immediately prior week, a Borrowing
Base Certificate as of the end of such prior week, together with such additional
Borrowing Base Certificates as and when requested by the Agent in writing.
Together with each such Borrowing Base Certificate, the Borrowers shall deliver:
(1) a schedule of the Borrowers’ Accounts created, credits given, cash
collected, and other adjustments to Accounts since the last such schedule;
(2) an aging of the Borrower’s Accounts, together with a reconciliation to the
corresponding Borrowing Base and to the Borrowers’ general ledger; (3) an aging
of the Borrowers’ accounts payable; (4) a detailed calculation and description
of Eligible Petroleum Inventory, DOE Contract Value, Eligible Cash and Eligible
Investments, Eligible In-Transit Petroleum Inventory, First Purchaser Liens, and
Paid but Unexpired Letters of Credit; (5) a schedule in reasonable detail
setting forth the additions and reductions in the Borrowers’ accounts receivable
since delivery of the previous Borrowing Base Certificate with a reconciliation
to the corresponding accounts receivable aging; and (6) Inventory reports by
category, together with reconciliation to the corresponding Borrowing Base and
to the Borrowers’ general ledger. Upon request of the Agent, the Borrowers shall
deliver: (A) inventory reports by location; (B) copies of invoices in connection
with the Borrowers’ Accounts, customer statements, credit memos, remittance
advices and reports, deposit slips, shipping and delivery documents in
connection with the Borrowers’ Accounts and for Inventory and Equipment acquired
by the Borrowers, purchase orders, and invoices; (C) a statement of the balance
of each intercompany Account, if any; (D) such other reports as to the
Collateral as the Agent shall reasonably request from time to time; and (E) with
the delivery of each of the foregoing, a certificate of the Borrower Agent
executed by an officer thereof certifying as to the accuracy and completeness of
the foregoing. If the Borrowers’ records or reports of the Collateral are
prepared by an accounting service or other agent, the Borrowers hereby authorize
such service or agent to deliver such records, reports, and related documents to
the Agent, for distribution to the Lenders.”
          (e) Amendment of Section 10.1.6 of the Loan Agreement.
Section 10.1.6(b) of the Loan

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Agreement is hereby amended and restated in its entirety as follows:
“ (b) Holdings and each Subsidiary will permit any representatives designated by
Agent or any Lender to visit and inspect the financial records and the
properties of such Person during regular business hours upon reasonable prior
notice and as often as reasonably requested and to make extracts from and copies
of such financial records, and permit any representatives designated by Agent or
any Lender to discuss the affairs, finances and condition of such Person with
the officers thereof and independent accountants therefor; provided, that
Holdings and each Subsidiary will reimburse Agent for all reasonable charges,
costs and expenses of Agent in connection with up to four examinations per Loan
Year of any Obligor’s books and records or any other financial or Collateral
matters as Agent deems appropriate, including, without limitation, Agent’s
standard charges of Agent’s outside appraisal group for any and all appraisals
conducted by or on behalf of Agent.”
     3. Acknowledgment of the Obligors. The Company and Holdings, as Obligors,
hereby acknowledge and agree that, to the best of their knowledge: (a) none of
the Obligors has any defense, offset, or counterclaim with respect to the
payment of any sum owed to the Lenders or the Agent under the Loan Documents, or
with respect to the performance or observance of any warranty or covenant
contained in the Loan Agreement or any of the other Loan Documents; and (b) the
Lenders and the Agent have performed all obligations and duties owed to the
Obligors through the date of this Amendment.
     4. Consent and Reaffirmation of Holdings Guaranty. Holdings hereby consents
to the foregoing amendment and acknowledges and agrees that nothing herein shall
in any way limit or diminish any of the obligations of Holdings under the
Holdings Guaranty, such Holdings Guaranty being hereby ratified and affirmed.
     5. Representations and Warranties of the Obligors. The Company and
Holdings, as Obligors, represent and warrant to the Lenders and the Agent that:
          (a) Compliance with Loan Agreement. On the date hereof, no Default or
Event of Default has occurred and is continuing;
          (b) Representations and Warranties. On the date hereof, and after
giving effect to this Amendment, the representations and warranties of each
Obligor in the Loan Documents are true and correct in all material respects
(except to the extent that such representations and warranties specifically
refer to an earlier date, in which case they are true and correct in all
material respects as of such earlier date);
          (c) Power and Authority. Each Obligor is duly authorized to execute,
deliver and perform this Amendment. The execution, delivery and performance of
this Amendment and the Loan Agreement, as amended hereby, have been duly
authorized by all necessary action, and do not (a) require any consent or
approval of the Term Loan Agent, other than those already obtained; (b)
contravene the Organic Documents of any Obligor; (c) violate or cause a default
under any Applicable Law or Material Contract; or (d) result in or require the
imposition of any Lien (other than Permitted Encumbrances) on any Property of
any Obligor; and
          (d) Enforceability. This Amendment and the Loan Agreement, as amended
hereby, are legal, valid and binding obligations of each Obligor, enforceable in
accordance with its terms, except as enforceability may be limited by
bankruptcy, insolvency or similar laws affecting the enforcement of creditors’
rights generally.

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     6. Effectiveness of this Amendment. The amendment of the Loan Agreement
will become effective (the “First Amendment Effective Date”) as of the date of
this Amendment upon the receipt by the Agent of this Amendment duly executed by
the Agent, the Lenders, the Company, and Holdings.
     7. Effect on Loan Agreement. Except as specifically amended hereby, the
terms and provisions of the Loan Agreement and the other Loan Documents are, in
all other respects, ratified and confirmed and remain in full force and effect.
No reference to this Amendment need be made in any notice, writing, or other
communication relating to the Loan Agreement and the other Loan Documents, any
such reference to the Loan Agreement and the other Loan Documents to be deemed a
reference thereto as respectively amended by this Amendment. All references to
the Loan Agreement and the other Loan Documents in any document, instrument, or
agreement executed in connection with the Loan Agreement and the other Loan
Documents will be deemed to refer to the Loan Agreement and the other Loan
Documents as respectively amended hereby.
     8. Fees and Expenses. The Company hereby agrees to pay all reasonable
out-of-pocket expenses incurred by the Agent in connection with the preparation,
negotiation, and consummation of this Amendment, and all other documents related
hereto, including without limitation, the reasonable fees and expenses of the
Lenders’ counsel.
     9. Successors. This Amendment will be binding upon and inure to the benefit
of the Company, Holdings, the Lenders, the Agent, and their respective
successors and assigns, provided, however, that no interest herein may be
assigned by the Company, Holdings, or any other Obligor without the prior
written consent of the Agent and each Lender.
     10. Governing Law. THIS AMENDMENT SHALL BE GOVERNED BY THE LAWS OF THE
STATE OF NEW YORK, WITHOUT GIVING EFFECT TO ANY CONFLICT OF LAW PRINCIPLES OTHER
THAN SECTION 5-1401 AND 5-1402 OF THE NEW YORK GENERAL OBLIGATIONS LAW OF THE
STATE OF NEW YORK (BUT GIVING EFFECT TO FEDERAL LAWS RELATING TO NATIONAL
BANKS).
     11. Consent to Forum; Arbitration. EACH OF THE COMPANY AND HOLDINGS, AS AN
OBLIGOR, HEREBY CONSENTS TO THE NON-EXCLUSIVE JURISDICTION OF ANY FEDERAL OR
STATE COURT SITTING IN OR WITH JURISDICTION OVER THE STATE OF NEW YORK, IN ANY
PROCEEDING OR DISPUTE RELATING IN ANY WAY TO THIS AMENDMENT, AND AGREES THAT ANY
SUCH PROCEEDING SHALL BE BROUGHT BY IT SOLELY IN ANY SUCH COURT. EACH OF THE
COMPANY AND HOLDINGS, AS AN OBLIGOR, IRREVOCABLY WAIVES ALL CLAIMS, OBJECTIONS
AND DEFENSES THAT IT MAY HAVE REGARDING SUCH COURT’S PERSONAL OR SUBJECT MATTER
JURISDICTION, VENUE OR INCONVENIENT FORUM. Nothing herein shall limit the right
of Agent or any Lender to bring proceedings against any Obligor in any other
court, nor limit the right of any party to serve process in any other manner
permitted by Applicable Law. Nothing in this Amendment shall be deemed to
preclude enforcement by Agent of any judgment or order obtained in any forum or
jurisdiction. Notwithstanding the foregoing, Section 14.14 of the Loan Agreement
is incorporated herein by reference and shall apply to this Amendment.
     12. Counterparts. This Amendment may be executed in counterparts, each of
which shall constitute an original, but all of which when taken together shall
constitute a single contract. Delivery of a signature page of any Loan Document
by telecopy or electronic mail shall be effective as delivery of a manually
executed counterpart of such agreement.
     13. Severability. Wherever possible, each provision of this Amendment shall
be interpreted

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in such manner as to be valid under Applicable Law. If any provision is found to
be invalid under Applicable Law, it shall be ineffective only to the extent of
such invalidity and the remaining provisions of this Amendment shall remain in
full force and effect.
     14. Entire Agreement. Time is of the essence of the Loan Documents. This
Amendment and the Loan Agreement, as amended hereby, and the other Loan
Documents constitute the entire contract among the parties relating to the
subject matter hereof, and supersede any and all previous agreements and
understandings, oral or written, relating to the subject matter hereof.
[Remainder of Page Intentionally Left Blank]

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     IN WITNESS WHEREOF, this Amendment has been executed and delivered as of
the date set forth above.

            COMPANY:

ALON REFINING KROTZ SPRINGS, INC.
      By:   /s/ Jeff D. Morris         Title: President and CEO               
HOLDINGS:

ALON REFINING LOUISIANA, INC.
      By:   /s/ Jeff D. Morris         Title: President and CEO               
AGENT AND LENDER:

BANK OF AMERICA, N.A.,
as Agent and a Lender
      By:   /s/ Todd R. Eggertsen 
Todd R. Eggertsen 
      Title:   Vice President