Document:

EX-4.1

 Exhibit 4.1 

THIRD AMENDMENT TO STOCKHOLDERS AGREEMENT 

THIS THIRD AMENDMENT (the “Third Amendment”) TO STOCKHOLDERS AGREEMENT is made and
entered into as of this 5th day of January, 2015, by and among Par Petroleum Corporation, a Delaware corporation (the “Company”), and certain holders of the Company’s common stock, $.01 par value per share
(“Common Stock”) listed on the signature pages hereto.  
 RECITALS: 

WHEREAS, pursuant to Section 6.8 of the Stockholders Agreement dated August 31, 2012 (as amended to date, the
“Stockholders Agreement”), by and among the Company, certain holders of the Common Stock listed on Schedule A thereto (the “Key Holders”), and any subsequent investors, or transferees, who
become parties thereto as “Investors” pursuant to Sections 6.1 and 6.2 of the Stockholders Agreement (the “Investors,” and together collectively with the Key Holders, the
“Stockholders”), the Stockholders Agreement may be amended or modified by the Company with the approval of the board of directors (the “Board”) of the Company and the holders of sixty-seven percent
(67%) of the Shares (as defined in the Stockholders Agreement) of Common Stock then held by the Key Holders; and 

WHEREAS, the Key Holders listed on the signature pages hereto desire to enter into the Third Amendment to amend their rights to designate
certain members of the Board, as well as certain related rights. 
 NOW, THEREFORE, the parties hereto agree to amend the Stockholders
Agreement as follows: 
  

	 	I.	Amendment to the Stockholders Agreement: 

 1.
Section 1.1 of the Stockholders Agreement is hereby amended and restated in its entirety and replaced with the following: 

“Size of the Board. Each Stockholder agrees to vote, or cause to be voted, all Shares (as defined below) owned by
such Stockholder, or over which such Stockholder has voting control, from time to time and at all times, in whatever manner as shall be necessary to ensure that the size of the Board shall be set and remain at nine (9) directors. For purposes
of this Agreement, the term “Shares” shall mean and include any securities of the Company the holders of which are entitled to vote for members of the Board, including without limitation, all shares of Common Stock, by
whatever name called, now owned or subsequently acquired by a Stockholder, however acquired, whether through stock splits, stock dividends, reclassifications, recapitalizations, similar events or otherwise.” 

 2. Section 1.2(d) of the Stockholders Agreement is hereby
amended and restated in its entirety and replaced with the following:  
 “Five (5) individuals
designated by the Board (collectively, the “Board Designees”); and” 
  

	 	II.	General Provisions 

 1. In case of conflict between this Third
Amendment and the Stockholders Agreement, this Third Amendment shall control. 
 2. The Stockholders Agreement, except as expressly amended
hereby, shall remain in full force and effect. 
 3. Incorporation of Certain Information by Reference. The provisions of Sections
6.4, 6.14 and 6.18 of the Stockholders Agreement captioned “Governing Law,” “Dispute Resolution” and “Costs of Enforcement,” respectively, are incorporated herein by reference as though such provisions were fully set
forth verbatim herein and shall apply to this Second Amendment mutatis mutandis. 
 4. Counterparts. This Third Amendment may
be executed in several counterparts (including by facsimile, .pdf or other electronic transmission), each of which shall be deemed an original and all of which together constitute one and the same instrument. 

[Signature appears on following page] 

  
 2 

 IN WITNESS WHEREOF, the parties have executed this Third Amendment to Stockholders Agreement as
of the date first written above. 
  

			
	COMPANY
	
	PAR PETROLEUM CORPORATION
		
	By:	 	 /s/ Christopher Micklas

	Name:	 	Christopher Micklas
	Title:	 	  

	
	KEY HOLDERS
	
	ZELL CREDIT OPPORTUNITIES FUND, L.P.
		
	By:	 	 /s/ Jon Wasserman

	Name:	 	Jon Wasserman
	Title:	 	Vice President
	
	ZCOF PAR PETROLEUM HOLDINGS, LLC
		
	By:	 	 /s/ Jon Wasserman

	Name:	 	Jon Wasserman
	Title:	 	Vice President
	
	WATERSTONE OFFSHORE ER FUND, LTD
		
	By:	 	Waterstone Capital Management, L.P.
		
	By:	 	  

	Name:	 	  

	Title:	 	  

 [SIGNATURE PAGE TO THIRD
AMENDMENT TO STOCKHOLDERS AGREEMENT] 

 
			
	 PRIME CAPITAL MASTER SPC, GOT

WAT MAC SEGREGATED PORTFOLIO

		
	By:	 	Waterstone Capital Management, L.P.
		
	By:	 	  

	Name:	 	  

	Title:	 	  

	
	WATERSTONE MARKET NEUTRAL MASTER FUND, LTD
		
	By:	 	Waterstone Capital Management, L.P.
		
	By:	 	  

	Name:	 	  

	Title:	 	  

	
	PANDORA SELECT PARTNERS, LP
		
	By:	 	Pandora Select Advisors, LLC
		 	its General Partner
		
	By:	 	Whitebox Advisors, LLC
		 	its Managing Partner
		
	By:	 	  

	Name:	 	  

	Title:	 	  

 [SIGNATURE PAGE TO SECOND
AMENDMENT TO STOCKHOLDERS AGREEMENT] 

			
	WHITEBOX MULTI-STRATEGY PARTNERS, LP
		
	By:	 	Whitebox Multi-Strategy Advisors, LLC
		 	its General Partner
		
	By:	 	Whitebox Advisors, LLC
		 	its Managing Partner
		
	By:	 	 /s/ Mark Strefling

	Name:	 	Mark Strefling
	Title:	 	General Counsel & Chief Operating Officer
	
	WHITEBOX CREDIT ARBITRAGE PARTNERS, LP
		
	By:	 	 Whitebox Credit Arbitrage Advisors, LLC
 its
General Partner

		
	By:	 	Whitebox Advisors, LLC
		 	its Managing Partner
		
	By:	 	 /s/ Mark Strefling

	Name:	 	Mark Strefling
	Title:	 	General Counsel & Chief Operating Officer
	
	WHITEBOX CONCENTRATED CONVERTIBLE ARBITRAGE PARTNERS, LP
		
	By:	 	Whitebox Advisors, LLC
		 	its Managing Partner
		
	By:	 	 /s/ Mark Strefling

	Name:	 	Mark Strefling
	Title:	 	General Counsel & Chief Operating Officer

 [SIGNATURE PAGE TO SECOND
AMENDMENT TO STOCKHOLDERS AGREEMENT] 

 
			
	WHITEBOX ASYMMETRIC PARTNERS, LP
		
	By:	 	Whitebox Asymmetric Advisors, LLC
		 	its General Partner
		
	By:	 	Whitebox Advisors, LLC
		 	its Managing Partner
		
	By:	 	 /s/ Mark Strefling

	Name:	 	Mark Strefling
	Title:	 	General Counsel & Chief Operating Officer

 [SIGNATURE PAGE TO SECOND
AMENDMENT TO STOCKHOLDERS AGREEMENT]EX-10.1

 Exhibit 10.1 

SECOND AMENDMENT OF 

AGREEMENT AND PLAN OF MERGER 

This Second Amendment of Agreement and Plan of Merger (this “Amendment”) is made and entered into as of
December 31, 2014 (the “Amendment Date”) by and among (a) Par Petroleum Corporation, a Delaware corporation (“Parent”), (b) Bogey, Inc., a Hawaii corporation and a wholly-owned, indirect
subsidiary of Parent (“Merger Sub”), (c) Koko’oha Investments, Inc., a Hawaii corporation (the “Company”), and (d) Bill D. Mills, in his capacity as the Shareholders’
Representative. Parent, Merger Sub, the Company and the Shareholders’ Representative are each referred to herein as a “Party” and collectively referred to herein as the “Parties”. 

RECITALS 

WHEREAS, the Parties entered into that certain Agreement and Plan of Merger dated as of June 2, 2014, as amended by that certain
Amendment to Agreement and Plan of Merger dated September 9, 2014 (the “Agreement”); 
 WHEREAS, the
Parties anticipate the HSR Waiting Period extending beyond January 1, 2015; and 
 WHEREAS, the Parties hereto desire to amend
the Agreement as provided below. 
 AGREEMENT 

NOW, THEREFORE, in consideration of the mutual covenants contained herein, and for other good and valuable consideration, the receipt
and sufficiency of which is hereby acknowledged, the Parties hereby agree as follows: 
 1. Defined Terms. All capitalized terms used
in this Amendment but not otherwise defined shall have their same meanings as set forth in the Agreement. 
 2. Final Termination
Date. Section 9.1(b) of the Agreement shall be amended in its entirety to read as follows: 
 “(b) by the Company or Parent, if
the Merger shall not have been consummated on or before March 31, 2015 (the “Final Termination Date”); provided, that the right to terminate this Agreement under this Section 9.1(b) shall not be
available to any party whose failure to fulfill any obligation under this Agreement has been the cause of, or resulted in, the failure of the Merger to be consummated by such date;” 

3. No Other Effect. Except as specifically set forth in this Amendment, the Agreement remains unmodified and in full force and effect.

 4. Counterparts; Signatures. This Amendment may be executed in any number of counterparts
and by each of the undersigned on separate counterparts, and each such counterpart shall be deemed to be an original, but all such counterparts put together shall constitute but one and the same Amendment. Signatures to this Amendment transmitted by
..pdf, electronic mail or other electronic means shall be treated as originals in all respects for purposes of this Amendment. 
 5.
Successors and Assigns. This Amendment shall be binding upon and shall inure to the benefit of the Parties hereto and their respective successors and assigns. 

[Remainder of Page Intentionally Left Blank. Signatures Follow on Next Page.] 

 The Parties have executed this Amendment as of the Amendment Date. 

 

			
	PARENT:
	
	PAR PETROLEUM CORPORATION
		
	By:	 	 /s/ James Matthew Vaughn

		 	 Name:  James Matthew Vaughn

		 	 Title:    Sr. Vice President and General Counsel

	
	MERGER SUB:
	
	BOGEY, INC.
		
	By:	 	 /s/ Eric Wright

		 	 Name:  Eric Wright

		 	 Title:    President

	
	COMPANY:
	
	KOKO’OHA INVESTMENTS, INC.
		
	By:	 	 /s/ Jim R. Yates

		 	 Name:  Jim R. Yates

		 	 Title:    President

	
	SHAREHOLDERS’ REPRESENTATIVE:
	
	 /s/ Bill D. Mills

	BILL D. MILLSEX-10.2

 Exhibit 10.2 

Special Award (4-Year Vesting) 

PAR PETROLEUM CORPORATION 
 AWARD
OF RESTRICTED STOCK 
 (Special Award) 

In this Award, Par Petroleum Corporation (the “Company”) grants to Joseph Israel (the
“Participant”), a Director or an Employee, Restricted Stock under the Par Petroleum Corporation 2012 Long Term Incentive Plan (“Plan”). This Award of Restricted Stock is governed by the terms of this
Award document and the Plan. All capitalized terms not defined in this Award shall have the meaning of such terms as provided in the Plan. 
  

	 	1.	The “Date of Grant” is January 5, 2015. 

  

	 	2.	The total number of shares of Restricted Stock granted is 27,829. 

  

	 	3.	The Restricted Stock granted in this Award shall vest as follows: 

 Subject to item 4 below,
Participant shall not become vested in any of the Restricted Stock granted unless he or she is continuously a Director of the Company or employed with the Company or a Company Affiliate from the Date of Grant through the Vesting Date, and
Participant may not sell, assign, transfer, exchange, pledge, encumber, gift, devise, hypothecate or otherwise dispose of any Restricted Stock until such Restricted Stock become Vested as provided herein. The transfer restrictions and substantial
risk of forfeiture imposed in the foregoing sentence shall lapse on the following “Vesting Dates” as to 25% of the Restricted Stock on the first anniversary of the Date of Grant and 25% on each of the second, third and fourth
anniversary of the Date of Grant. The Restricted Stock as to which such restrictions so lapse are referred to as “Vested.” 
  

	 	4.	Other Vesting Events are as follows: 

 Notwithstanding the foregoing vesting schedule in item
3, the Restricted Stock will be 100% Vested upon any one of the following “Vesting Events”: (a) Participant’s termination as Director and Service due to death or Disability or termination of employment with the
Company and its Affiliates due to death or Disability, (b) the Participant’s termination of employment by the Company and its Affiliates without Cause or (c) upon a Change in Control. The date of the Participant’s termination of
directorship and Service or termination of employment with the Company and its Affiliates on account of one of the Vesting Events shall be the Vesting Date for purposes of this Award. The date of the Change in Control shall be the Vesting Date for
purposes of this Award. 
  

	 	5.	Other Terms and Conditions: 

 (a) No Fractional Shares. All provisions of this
Award concern whole shares of Stock. If the application of any provision hereunder would yield a fractional share, such fractional share shall be rounded down to the next whole share if it is less than 0.5 and rounded up to the next whole share if
it is 0.5 or more. 

 (b) Not an Employment or Service Agreement. This Award is not an employment
agreement, and this Award shall not be, and no provision of this Award shall be construed or interpreted to create any right of Participant to continue as a Director or continue employment with or provide services to the Company or any of its
Affiliates. 
 (c) Independent Tax Advice and Acknowledgments. Participant has been advised and Participant hereby
acknowledges that he or she has been advised to obtain independent legal and tax advice regarding this Award, the grant of the Restricted Stock and the disposition of such shares, including, without limitation, the election available under
Section 83(b) of the Internal Revenue Code. Participant acknowledges receipt of a copy of the Plan and represents that he or she is familiar with the terms and provisions thereof, and hereby accepts this Award subject to all the terms and
provisions of the Plan and this Award. 
 (d) The Committee has determined in connection with this Award that in the event
that a Section 83(b) election is not made, the Participant who is an Employee may elect to have the Company withhold that number of shares of Restricted Stock otherwise deliverable to the Participant when such shares become Vested or to deliver
to the Company a number of shares of Stock, in each case, having a Fair Market Value on the date of Vesting equal to the minimum amount required to be withheld for taxes as a result of such exercise. The election must be made in writing and must be
delivered to the Company prior to the date of Vesting. If the number of shares so determined shall include a fractional share, the Participant shall deliver cash in lieu of such fractional share. All elections shall be made in a form approved by the
Committee and shall be subject to disapproval, in whole or in part by the Committee. 
 The Restricted Stock granted hereunder will be
subject to all applicable federal, state and local taxes domestic and foreign and withholding requirements (including, without limitation, any withholding required under any other employee benefit plan maintained by the Company or a Company
Affiliate). The Participant hereby agrees to accept as binding, conclusive, and final all decisions or interpretations of the Committee or the Board, as appropriate, upon any questions arising under the Plan or this Award. 

 

			
	PARTICIPANT:   Joseph Israel
		
	Signature:	 	/s/ Joseph Israel
	Date: January 5, 2015

 
			
	
	PAR PETROLEUM CORPORATION
		
	By:	 	/s/ Christopher Micklas
		 	Christopher Micklas
	Date: January 5, 2015

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