exv4w1





 Exhibit 4.1

HOLLYFRONTIER CORPORATION

(successor-in-interest to Frontier Oil Corporation),




as Issuer,



THE GUARANTORS NAMED HEREIN



and



WELLS FARGO BANK, NATIONAL ASSOCIATION,



as Trustee



THIRD SUPPLEMENTAL INDENTURE



dated as of July 1, 2011



to Indenture dated as of November 22, 2010



Providing for Issuance of



67⁄8% Senior Notes due 2018








 









 








THIRD SUPPLEMENTAL INDENTURE




     This THIRD SUPPLEMENTAL INDENTURE (this “Third Supplemental Indenture”), dated as
of July 1, 2011, among HOLLYFRONTIER CORPORATION, a Delaware corporation and successor-in-interest
to Frontier Oil Corporation (the “Company”), the Guarantors and WELLS FARGO BANK, N.A., a
national banking association, as Trustee (the “Trustee”), under the Indenture, dated as of
November 22, 2010, as supplemented by the First Supplemental Indenture, dated November 22, 2010 and
the Second Supplemental Indenture, dated May 26, 2011 (collectively, the “Indenture”).
Capitalized terms used herein and not otherwise defined shall have the meaning assigned to them in
the Indenture.



     WHEREAS, the Frontier Oil Corporation (“FOC”), predecessor-in-interest to the Company
entered into an Agreement and Plan of Merger, dated as of February 21, 2011, with the Company, and
North Acquisition, Inc., a Delaware corporation and direct wholly owned subsidiary of the Company
(“Merger Sub”), pursuant to which, effective at 12:01 a.m. MDT on July 1, 2011, Merger Sub
merged with and into FOC, with FOC being the surviving corporation of such merger (the
“Merger”);



     WHEREAS, following the Merger, on the date hereof, FOC merged with and into the Company, with
the Company surviving such merger;



     WHEREAS, the Company has agreed, pursuant to Section 8.2 of the Indenture, to assume all of
FOC’s indebtedness outstanding under the 67⁄8% Notes and the Indenture;



     WHEREAS, certain Restricted Subsidiaries of the Company have agreed to provide a guarantee (a
“Guarantee”) to comply with Section 10.17 of the Indenture, and Section 9.1(6) of the
Indenture provides that the Company and the Trustee may amend or supplement the Indenture for such
purpose without the consent of the Holders of the 67⁄8% Notes;



     WHEREAS, Frontier Holdings LLC (f/k/a Frontier Holdings Inc.), a Delaware limited liability
company and a Guarantor of the 67⁄8% Notes, has merged with and into Eagle Consolidation LLC, a
Delaware limited liability company and a Guarantor of the 67⁄8% Notes by the execution of this Third
Supplemental Indenture (“ECLLC”), all in accordance with Section 14.4 of the Indenture;



     WHEREAS, Frontier Oil and Refining Company LLC (f/k/a Frontier Oil and Refining Company), a
Delaware limited liability company and a Guarantor of the 67⁄8% Notes, has merged with and into
HollyFrontier Refining & Marketing LLC (f/k/a Holly Refining & Marketing LLC), a Delaware limited
liability company and a Guarantor of the 67⁄8% Notes (“HFRMLLC”) by the execution of this
Third Supplemental Indenture, all in accordance with Section 14.4 of the Indenture; and



     WHEREAS, all acts and things prescribed by the Indenture, by law and by the certificate of
incorporation and the bylaws or comparable constituent documents of the Company, of the Guarantors
and of the Trustee necessary to make this Third Supplemental Indenture a valid instrument legally
binding on the Company, the Guarantors and the Trustee, in accordance with its terms, have been
duly done and performed;



     NOW, THEREFORE, to comply with the provisions of the Indenture and in consideration of the
above premises, the Company, the Guarantors and the Trustee covenant and agree for the equal and
proportionate benefit of the respective Holders of the 6 7/8% Notes as follows:



1









 





ARTICLE 1




     Section 1.01. This Third Supplemental Indenture is supplemental to the Indenture and does and
shall be deemed to form a part of, and shall be construed in connection with and as part of, the
Indenture for any and all purposes.



     Section 1.02. This Third Supplemental Indenture shall become effective immediately upon its
execution and delivery by each of the Company, the Guarantors and the Trustee.



ARTICLE 2




     Section 2.01. From this date, in accordance with Section 8.2 of the Indenture, and by
executing this Third Supplemental Indenture, the Company hereby assumes all of the obligations of
FOC under the 67⁄8% Notes and the Indenture.



     Section 2.02. From this date, in accordance with Section 14.4 of the Indenture, and by
executing this Third Supplemental Indenture and the accompanying notation of Guarantee (a copy of
which is attached hereto), each of ECLLC and HFRMLLC hereby assumes all of the obligations of FHLLC
and FORCLLC, respectively, under the applicable Subsidiary Guaranty.



     Section 2.03. From this date, in accordance with Section 10.17 of the Indenture, and by
executing this Third Supplemental Indenture and the accompanying notation of Guarantee (a copy of
which is attached hereto), the Guarantors whose signatures appear below are subject to the
provisions of the Indenture to the extent provided for in Article Fourteen thereunder.



ARTICLE 3




     Section 3.01. Except as specifically modified herein, the Indenture and the 67⁄8% Notes are in
all respects ratified and confirmed (mutatis mutandis) and shall remain in full force and effect in
accordance with their terms.



     Section 3.02. Except as otherwise expressly provided herein, no duties, responsibilities or
liabilities are assumed, or shall be construed to be assumed, by the Trustee by reason of this
Third Supplemental Indenture. This Third Supplemental Indenture is executed and accepted by the
Trustee subject to all of the terms and conditions set forth in the Indenture with the same force
and effect as if those terms and conditions were repeated at length herein and made applicable to
the Trustee with respect hereto. The Trustee makes no representation as to the validity or
sufficiency of this Third Supplemental Indenture and shall not be responsible for or with respect
to any of the recitals or statements contained herein, all of which recitals or statements are made
solely by the Company and the Guarantors.



     Section 3.03. THE LAW OF THE STATE OF NEW YORK SHALL GOVERN AND BE USED TO CONSTRUE AND
ENFORCE THIS THIRD SUPPLEMENTAL INDENTURE WITHOUT GIVING EFFECT TO APPLICABLE PRINCIPLES OF
CONFLICT OF LAW TO THE EXTENT THAT THE APPLICATION OF THE LAWS OF ANOTHER JURISDICTION WOULD BE
REQUIRED THEREBY.



     Section 3.04. The parties may sign any number of copies of this Third Supplemental Indenture.
Each signed copy shall be an original, but all of such executed copies together shall represent the
same agreement.



[SIGNATURE PAGES FOLLOW]



2









 





     IN WITNESS WHEREOF, the parties hereto have caused this Third Supplemental Indenture to be
duly executed, all as of the date first written above.



	 	 	 	 	 
	 	Issuer:



HOLLYFRONTIER CORPORATION

 	 
	 	By:  	 /s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President & Chief Executive Officer 	 
	 
	 	Guarantors:



FRONTIER REFINING & MARKETING LLC

FRONTIER REFINING LLC

FRONTIER EL DORADO REFINING LLC

FRONTIER PIPELINE LLC

ETHANOL MANAGEMENT COMPANY LLC

 	 
	 	By:  	 /s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President 	 
	 
	 	

BLACK EAGLE LLC

 	 
	 	By:  	 /s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	EAGLE CONSOLIDATION LLC

 	 
	 	By:  	 /s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY BIOFUELS LLC

 	 
	 	By:  	 /s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 



3









 






	 	 	 	 	 



	 	 	 	 	 
	 	HOLLYFRONTIER PAYROLL SERVICES, INC.

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY PETROLEUM, INC.

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY REALTY, LLC

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLYFRONTIER REFINING & MARKETING LLC

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY REFINING & MARKETING — TULSA LLC

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY REFINING & MARKETING —
WOODS CROSS LLC

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 




4











 





	 	 	 	 	 
	 	HOLLY REFINING COMMUNICATIONS INC.

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY TRANSPORTATION LLC

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY UNEV PIPELINE COMPANY

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY WESTERN ASPHALT COMPANY

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLYMARKS, LLC

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HRM REALTY, LLC

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 



5









 






	 	 	 	 	 



	 	 	 	 	 
	 	LEA REFINING COMPANY

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO HOLDINGS, INC.

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO PIPELINE CO., L.P.

 	 
	 	By:  	Navajo Pipeline G.P., L.L.C.
 	 
	 	 	Its General Partner 	 
	 	 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO PIPELINE GP, L.L.C.

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO PIPELINE LP, L.L.C.

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO REFINING COMPANY, L.L.C.

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 



6









 






	 	 	 	 	 



	 	 	 	 	 
	 	NAVAJO REFINING GP, L.L.C.

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO WESTERN ASPHALT COMPANY

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NK ASPHALT PARTNERS,

DBA HOLLY ASPHALT COMPANY

 	 



	 	 	 	 	 
	 	HOLLY WESTERN ASPHALT COMPANY,

PARTNER

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO WESTERN ASPHALT COMPANY,

PARTNER

 	 
	 	By:  	/s/ Michael C. Jennings	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 



	 	 	 	 	 
	 	Trustee:


WELLS FARGO BANK, N.A., as Trustee

 	 
	 	By:  	/s/ Patrick T. Giordano	 
	 	 	Name:  	Patrick T. Giordano 	 
	 	 	Title:  	Vice President 	 
	 




7











 





NOTATION OF SUBSIDIARY GUARANTEE



Each of the Guarantors (which term includes any successor Person in such capacity under the
Indenture), has fully, unconditionally and absolutely guaranteed, to the extent set forth in the
Indenture and subject to the provisions in the Indenture, the due and punctual payment of the
principal of, and premium, if any, and interest on the 67⁄8% Notes and all other amounts due and
payable under the Indenture and the 67⁄8% Notes by the Company.



The obligations of the Guarantors to the Holders of 67⁄8% Notes and to the Trustee pursuant to the
Subsidiary Guarantees and the Indenture are expressly set forth in Article Fourteen of the
Indenture and reference is hereby made to the Indenture for the precise terms of the Subsidiary
Guarantees.




	 	 	 	 	 
	 	Guarantors:



BLACK EAGLE LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	EAGLE CONSOLIDATION LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY BIOFUELS LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLYFRONTIER PAYROLL SERVICES, INC.

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY PETROLEUM, INC.

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 



 









 






	 	 	 	 	 



	 	 	 	 	 
	 	HOLLY REALTY, LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLYFRONTIER REFINING & MARKETING LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY REFINING & MARKETING — TULSA LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY REFINING & MARKETING -

WOODS CROSS LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY REFINING COMMUNICATIONS INC.

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY TRANSPORTATION LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 



 









 






	 	 	 	 	 



	 	 	 	 	 
	 	HOLLY UNEV PIPELINE COMPANY

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLY WESTERN ASPHALT COMPANY

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HOLLYMARKS, LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	HRM REALTY, LLC

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	LEA REFINING COMPANY

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO HOLDINGS, INC.

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 



 









 






	 	 	 	 	 



	 	 	 	 	 
	 	NAVAJO PIPELINE CO., L.P.

 	 
	 	  	
 	 
	 	By: 	Navajo Pipeline G.P., L.L.C. 	 
	 	 	Its General Partner 	 
	 
	 	 	 
	 	By:  	
/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO PIPELINE GP, L.L.C.

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO PIPELINE LP, L.L.C.

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO REFINING COMPANY, L.L.C.

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO REFINING GP, L.L.C.

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 
	 
	 	NAVAJO WESTERN ASPHALT COMPANY

 	 
	 	By:  	/s/ Michael C. Jennings 	 
	 	 	Name:  	Michael C. Jennings 	 
	 	 	Title:  	President and Chief Executive Officer 	 



 









 






	 	 	 	 	 



	 	 	 	 	 	 
	 	NK ASPHALT PARTNERS,

DBA HOLLY ASPHALT COMPANY

 	 
	 	 	
HOLLY WESTERN ASPHALT COMPANY,

PARTNER

 
	 		By:  	 /s/ Michael C. Jennings	 
	 	 		Name:  	Michael C. Jennings 	 
	 	 		Title:  	President and Chief Executive Officer 	 
	 	
	 	 	NAVAJO WESTERN ASPHALT COMPANY,

PARTNER

 	 
	 		By:  	 /s/ Michael C. Jennings	 
	 	 		Name:  	Michael C. Jennings 	 
	 	 		Title:  	President and Chief Executive Officer