UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549


SCHEDULE 13D
(Amendment No. 2)

Under the Securities Exchange Act of 1934*

Alon USA Energy, Inc.
(Name of Issuer)

Common Stock, par value $0.01 per share
(Title of Class of Securities)

020520102
(CUSIP Number)

Kent B. Thomas
Delek US Holdings, Inc.
7102 Commerce Way
Brentwood, Tennessee 37027
(615) 771-6701
(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

January 29, 2016
(Date of Event which Requires Filing of this Statement)



If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box. ¨



Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See § 240.13d-7 for other parties to whom copies are to be sent.


*
The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

(Continued on Following Pages)







TABLE OF CONTENTS

 
 
Introductory Note
Item 4.
 
Purpose of Transaction.
Item 5.
 
Interest in Securities of the Issuer.
Item 7
 
Items to be filed as Exhibits
 
 
Signature







CUSIP NO. 020520102
 
13D
 
 

1
 
 
NAME OF REPORTING PERSONS.
I.R.S. Identification No. of above persons (entities only).

Delek US Holdings, Inc.
2
 
 
CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)
(a) o        (b) x

3
 
 
SEC USE ONLY

4
 
 
SOURCE OF FUNDS (SEE INSTRUCTIONS)

BK, WC, OO
5
 
 
CHECK IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) OR 2(e)

o
6
 
 
CITIZENSHIP OR PLACE OF ORGANIZATION

Delaware
NUMBER OF
SHARES
BENEFICIALLY
OWNED BY
EACH
REPORTING
PERSON
WITH

 
7
 
 
SOLE VOTING POWER

33,691,292
 
8
 
 
SHARED VOTING POWER

0
 
9
 
 
SOLE DISPOSITIVE POWER

33,691,292
 
10
 
SHARED DISPOSITIVE POWER

0
11
 
AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

33,691,292
12
 
CHECK IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES (SEE INSTRUCTIONS)

o
13
 
PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

47.5% based on 70,960,461 shares outstanding as of October 30, 2015
14
 
TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)

CO







Introductory Note

This Amendment No. 2 to Schedule 13D (“Amendment No. 2”) is filed by Delek US Holdings, Inc. (“Delek”), a Delaware corporation, to amend the Schedule 13D related to the common stock, par value $0.01 per share, of Alon USA Energy, Inc. (“Alon USA”) previously filed by Delek with the United States Securities and Exchange Commission on May 26, 2015 (the “Initial 13D”) and amended on December 23, 2015 ("Amendment No. 1"). Each capitalized term used and not otherwise defined herein shall have the meaning assigned to such term in the Initial 13D and Amendment No. 1. Except as otherwise provided herein, each Item of the Initial 13D and Amendment No. 1 remain unchanged.

Item 4. Purpose of Transaction

Item 4 is hereby supplemented to add the following:

On January 29, 2016, Delek US Holdings, Inc. (“Delek”) and Alon USA Energy, Inc. (“Alon USA”) entered into a first amendment (the “First Amendment”) to that certain Amended and Restated Stockholder Agreement between them dated April 14, 2015 (the “Stockholder Agreement”). Among other terms, the First Amendment:

(a)
Confirms that the board of directors of Alon USA (the "Alon Board") has determined that the members of the Alon Board who are also employees of Delek are “independent directors” under Section 303A.02 of the New York Stock Exchange Listed Company Manual;

(b)
Confirms that the Stockholder Agreement will terminate on May 14, 2016;

(c)
Confirms the identity or criteria for selection of the slate of eleven director nominees to be proposed for election to the Alon Board at the 2016 annual meeting of Alon USA stockholders along with procedures to identify any vacancies in that slate of nominees that may occur; and

(d)
Confirms that Alon USA has amended its bylaws to extend certain voting requirements regarding the removal or replacement of the chairman of the Alon Board until the 2017 annual meeting of Alon USA stockholders.

Except as disclosed above, Delek does not have any present plans or proposals that relate to or would result in any of the actions required to be described under subparagraphs (a) through (j) of Item 4 of Schedule 13D. Delek may, at any time, review or reconsider its position with respect to a Potential Business Combination or otherwise with respect to Alon USA, and formulate plans or proposals with respect to any such matters.

Item 5. Interest in Securities of the Issuer.

Item 5 is hereby supplemented to add the following:

(a) — The information contained on the cover pages to this Schedule 13D are incorporated herein by reference.

Item 7. Items to be filed as Exhibits.

99.1
First Amendment dated January 29, 2016 to Amended and Restated Stockholder Agreement dated April 14, 2015, by and between Delek US Holdings, Inc. and Alon USA Energy, Inc.






Signature

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

DELEK US HOLDINGS, INC.

 
By: /s/ Kent B. Thomas
Date: February 3, 2016
Kent B. Thomas
 
Executive Vice President, General Counsel & Secretary
 

The original statement shall be signed by each person on whose behalf the statement is filed or his authorized representative. If the statement is signed on behalf of a person by his authorized representative (other than an executive officer or general partner of this filing person), evidence of the representative’s authority to sign on behalf of such person shall be filed with the statement, provided, however, that a power of attorney for this purpose which is already on file with the Commission may be incorporated by reference. The name and any title of each person who signs the statement shall be typed or printed beneath his signature.

Attention: Intentional misstatements or omissions of fact constitute Federal criminal violations (See 18 U.S.C. 1001).





Exhibit 99.1

FIRST AMENDMENT
TO
AMENDED AND RESTATED STOCKHOLDER AGREEMENT

This First Amendment, dated as of January 29, 2016 (this “First Amendment”), is entered into by and between Alon USA Energy, Inc., a Delaware corporation (the “Company”), and Delek US Holdings, Inc., a Delaware corporation (“Delek”). This First Amendment is an amendment to that certain Amended and Restated Stockholder Agreement, dated as of April 14, 2015 (the “Agreement”), by and between the Company and Delek.
WHEREAS, the Company and Delek desire to amend the Agreement with respect to the matters set forth herein; and
WHEREAS, in reliance on the Company’s covenants and agreements made in this First Amendment, Delek has decided not to submit a written notice of nominations of persons for election as directors of the Company at the 2016 annual meeting of Company stockholders as provided in Section 13 of the Amended and Restated Bylaws of the Company.
NOW, THEREFORE, in consideration of the foregoing and the mutual covenants and agreements contained herein, and intending to be legally bound hereby, the Company and Delek hereby agree as follows:
Section 1. Amendments.
(a) The parenthetical in Section 1.06(a) of the Agreement is hereby amended and restated to read in its entirety as follows:
(and, for purposes of satisfying this requirement, the Additional Directors shall be considered Independent Directors until the 2016 annual meeting of Company stockholders)
(b) The second parenthetical in Section 1.06(c) of the Agreement is hereby amended and restated to read in its entirety as follows:
(and, for purposes of satisfying this requirement, the Additional Directors shall be considered Independent Directors until the 2016 annual meeting of Company stockholders)
(c) The Agreement is hereby amended to add a new Section 1.07(e) (and a new Exhibit F, which is attached hereto as Exhibit F and incorporated by reference in new Section 1.07(e)) to read in its entirety as follows:
(e)    The Company represents and warrants to Delek that the Board of Directors has adopted the resolution(s) attached as Exhibit F pursuant to which it determined that the Delek Directors serving on


Exhibit 99.1

the Board of Directors at the time such resolutions were adopted are “independent directors” (as defined in NYSE rules and regulations).
(d) The Agreement is hereby amended to add a new Section 3.01(f) to read in its entirety as follows:
(f)    The Company represents and warrants to Delek that the Board of Directors has duly adopted the 2016 Amendment Resolutions.
(e) The Agreement is hereby amended to add to Section 4 a new definition of the term “2016 Amendment Resolutions” (and a new Exhibit G, which is attached hereto as Exhibit G and incorporated by reference in the new definition of 2016 Amendment Resolutions) to read in its entirety as follows:
“2016 Amendment Resolutions” means the duly adopted resolutions of the Board of Directors in the form attached hereto as Exhibit G.
(f) Section 6.09(c) of the Agreement is hereby amended and restated to read in its entirety as follows:
(c)    This Agreement shall terminate automatically, and without any further action, upon the first anniversary of the Closing.
(g) The Agreement is hereby amended (i) to renumber Section 6.14 as Section 6.15 and (ii) to add a new Section 6.14 (and a new Exhibit H, which is attached hereto as Exhibit H and incorporated by reference in new Section 6.14) to read in its entirety as follows:
SECTION 6.14    2016 Annual Meeting Matters.
Notwithstanding any other provision in this Agreement to the contrary:
(a)    In connection with the 2016 annual meeting of Company stockholders, the number of directorships constituting the Board of Directors shall be 11, and the Company and the Board of Directors shall nominate as the slate of 11 directors of the Company for election as directors at the 2016 annual meeting of Company stockholders (and shall recommend the stockholders vote in favor of) the persons listed or selected in accordance with the procedures described herein or on Exhibit H (the “2016 Director Nominees”).
(b)    If any of the 2016 Director Nominees become unavailable to stand for election or serve as a director of the Company prior to the 2016 annual meeting of stockholders, his or her replacement shall be selected as follows:

2


Exhibit 99.1

(i)    the person or persons to replace any of the persons identified in 1 through 4 on Exhibit H shall be selected by the Independent Nominating Committee, shall qualify to be Independent Directors and shall be reasonably acceptable to Delek;
(ii)    the person or persons to replace any of the persons identified in 5 through 9 on Exhibit H shall be selected by Delek and shall be reasonably acceptable to the Independent Nominating Committee in its good faith judgment to serve as a director of the Company; provided that the fact that a person is serving or has served as an officer or director of Delek or its Affiliates, in and of itself, shall not cause such person to be unacceptable to the Independent Nominating Committee; and
(iii)    the person or persons identified or to be identified in 10 and 11 on Exhibit H and any person or persons selected to replace any of such persons identified in 10 and 11 on Exhibit H shall be a person submitted to the Independent Nominating Committee by Delek who qualifies as an Independent Director and is reasonably acceptable to the Independent Nominating Committee in its good faith judgment to serve as a director of the Company.
(c)    The Company shall include the 2016 Director Nominees in the notice of the 2016 annual meeting of Company stockholders and in the proxy statement and on the proxy card distributed by the Company to Company stockholders in connection therewith, and shall recommend that the Company stockholders vote in favor of the 2016 Director Nominees.
(d)    The Company shall take all steps necessary for the due and proper noticing and calling at the 2016 annual meeting of the Company stockholders and the holding of such meeting on or about May 3, 2016 including, without limitation, the establishment of an appropriate record date for such meeting, and the distribution of the notice of and the proxy statement for such meeting all in each case consistent with the Company’s past practices.
Section 2. Authorization, etc.
(a) The Company represents and warrants to Delek that (i) the execution and delivery of this First Amendment by the Company have been duly authorized by all necessary corporate action on the part of the Company (including, without limitation, advance Independent Director Approval and advance approval of the Board of Directors) and no other corporate proceedings on the part of the Company are necessary to authorize this First Amendment and (ii) this First Amendment has been duly executed and delivered by the Company and constitutes a valid and

3


Exhibit 99.1

binding obligation of the Company, and is enforceable against the Company in accordance with its terms.
(b) Delek represents and warrants to the Company that (i) the execution and delivery of this First Amendment by Delek have been duly authorized by all necessary corporate action on the part of Delek and no other corporate proceedings on the part of Delek are necessary to authorize this First Amendment and (ii) this First Amendment has been duly executed and delivered by Delek and constitutes a valid and binding obligation of Delek, and is enforceable against Delek in accordance with its terms.
Section 3. Status. This First Amendment amends the Agreement, but only to the extent expressly set forth herein. All other provisions of the Agreement remain in full force and effect. Unless otherwise defined herein, initially capitalized terms have the meaning given them in the Agreement. If any provision of this First Amendment is inconsistent with any provision of the Agreement, the provision of this First Amendment shall control.
Section 4. Governing Law. This First Amendment shall be construed in accordance with and governed by the laws of the State of Delaware.
Section 5. Counterparts; Effectiveness. This First Amendment may be signed in any number of counterparts, each of which shall be an original, with the same effect as if the signatures thereto and hereto were upon the same instrument. This First Amendment shall become effective when each party hereto shall have received counterparts thereof signed by the other party hereto.
Section 6. Severability. If any term, provision, covenant or restriction of this First Amendment is held by a court of competent jurisdiction to be invalid, void or unenforceable, the remainder of the terms, provisions, covenants and restrictions of this First Amendment shall remain in full force and effect and shall in no way be affected, impaired or invalidated, provided that the parties hereto shall negotiate in good faith to attempt to place the parties in the same position as they would have been in had such provision not been held to be invalid, void or unenforceable.
Section 7. Further Assurances. Delek and the Company shall cooperate and take such action as may be reasonably requested by the other party in order to carry out the provisions and purposes of this First Amendment; provided, however, that neither Delek nor the Company shall be obligated to take any actions or omit to take any actions that would be inconsistent with applicable Law.
[Signature Pages Follow]

4




IN WITNESS WHEREOF, the parties hereto have caused this First Amendment to Amended and Restated Stockholder Agreement to be executed as of the date first referred to above.

DELEK US HOLDINGS, INC.



By:    /s/ Fredererc Green                
Name:    Frederec Green
Title:    EVP


By:    /s/ Kent B. Thomas                
Name:    Kent B. Thomas
Title:    General Counsel



ALON USA ENERGY, INC.



By:    /s/ Shai Even                    
Name:    Shai Even
Title:    SVP & CFO



5




Exhibit F

NYSE Independence Resolutions

[Capitalized terms used in the resolution are appropriately defined in the full resolutions.]

WHEREAS, the Nominating and Corporate Governance Committee has affirmatively determined that none of the following directors have disclosed any relationship that would disqualify such directors from being found to be independent under the applicable rules of the New York Stock Exchange:

Ezra Uzi Yemin
Frederec Green
Assaf Ginzburg
Avigal Soreq
Mark Smith

(the “Considered Directors”); and

WHEREAS, that the Nominating and Corporate Governance Committee has recommended that the Board of Directors make a determination as to the independence of each of the Considered Directors under the applicable rules of the New York Stock Exchange;

NOW THEREFORE BE IT RESOLVED, the Board has determined that the Considered Directors have no material relationship with the Company (either directly or as a partner, stockholder or officer of an organization that has a relationship with the Company) and qualify as independent directors pursuant to Section 303A.02 of the NYSE Listed Company Manual.



6




Exhibit G
2016 Amendment Resolutions
[Capitalized terms used in the resolution are appropriately defined in the full resolutions.]
RESOLVED that:
(i) effective immediately, the proviso at the end of the second sentence of Bylaw 17 of the Amended and Restated Bylaws of the Company (the “Bylaws”) is hereby amended to replace “2016 Annual Meeting of Stockholders” with “2017 Annual Meeting of Stockholders”; and
(ii) effective immediately, the proviso at the end of the second sentence of Bylaw 27 of the Bylaws is hereby amended to replace “2016 Annual Meeting of Stockholders” with “2017 Annual Meeting of Stockholders”.


7




Exhibit H

Director Nominees for the 2016 Annual Meeting

1.    Ron W. Haddock
2.    Zalman Segal
3.    Ilan Cohen
4.
David Wiessman
5.    Ezra Uzi Yemin
6.    Assaf Ginzburg
7.    Frederec Green
8.    Avigal Soreq
9.    Mark D. Smith
10.    TBD Independent
11.    TBD Independent

“TBD Independent” means a person who qualifies as an Independent Director submitted to the Independent Nominating Committee by Delek and reasonably acceptable to the Independent Nominating Committee in its good faith judgment to serve as a director of the Company.

8

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