EX-4.1


 Exhibit 4.1 

SECOND AMENDMENT TO STOCKHOLDERS AGREEMENT 

THIS SECOND AMENDMENT (the “Second Amendment”) TO STOCKHOLDERS AGREEMENT is made and entered into as of this
16th day of September, 2014, 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 Second 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 eight (8) 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: 
 “Four (4) individuals designated by the Board (collectively, the “Board
Designees”); and” 






 II. General Provisions 

1. In case of conflict between this Second Amendment and the Stockholders Agreement, this Second 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 Second 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 Second Amendment to Stockholders Agreement as
of the date first written above. 
  

			
	COMPANY
	
	PAR PETROLEUM CORPORATION
		
	By:	 	 /s/ Will Monteleone

	Name:	 	Will Monteleone
	Title:	 	CEO & President
	
	KEY HOLDERS
	
	ZELL CREDIT OPPORTUNITIES FUND, L.P.
		
	By:	 	Chai Trust Company, LLC
	Its:	 	General Partner
		
	By:	 	 /s/ Philip G. Tinkler

	Name:	 	Philip G. Tinkler
	Title:	 	Vice President
	
	ZCOF PAR PETROLEUM HOLDINGS, LLC
		
	By:	 	 /s/ Philip G. Tinkler

	Name:	 	Philip G. Tinkler
	Title:	 	Vice President
	
	WATERSTONE OFFSHORE ER FUND, LTD
		
	By:	 	Waterstone Capital Management, L.P.
		
	By:	 	 /s/ Martin Kalish

	Name:	 	Martin Kalish
	Title:	 	COO


  

  
 [SIGNATURE
PAGE TO FIRST AMENDMENT TO STOCKHOLDERS AGREEMENT] 








			
	PRIME CAPITAL MASTER SPC, GOT
	WAT MAC SEGREGATED PORTFOLIO
		
	By:	 	Waterstone Capital Management, L.P.
		
	By:	 	 /s/ Martin Kalish

	Name:	 	Martin Kalish
	Title:	 	COO
	
	WATERSTONE MARKET NEUTRAL
	MASTER FUND, LTD
		
	By:	 	Waterstone Capital Management, L.P.
		
	By:	 	 /s/ Martin Kalish

	Name:	 	Martin Kalish
	Title:	 	COO
	
	PANDORA SELECT PARTNERS, LP
		
	By:	 	Pandora Select Advisors, LLC
		 	its General Partner
		
	By:	 	Whitebox Advisors, LLC
		 	its Managing Partner
		
	By:	 	 /s/ Mark Strefling

	Name:	 	Mark Strefling
	Title:	 	Chief Operating Officer


  

  
 [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:	 	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 Stefling

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

	Name:	 	Mark Strefling
	Title:	 	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:	 	Chief Operating Officer


  

  
 [SIGNATURE
PAGE TO SECOND AMENDMENT TO STOCKHOLDERS AGREEMENT]