Second Supplemental Indenture



 Exhibit 4.11 
 SECOND SUPPLEMENTAL INDENTURE 
 SECOND
SUPPLEMENTAL INDENTURE (this “Second Supplemental Indenture”), dated as of July 18, 2011, among Holly Biofuels LLC, a Delaware limited liability company (“Holly Biofuels”), Ethanol
Management Company LLC, a Delaware limited liability company (“Ethanol Management”), Frontier El Dorado Refining LLC, a Delaware limited liability company (“Frontier El Dorado”), Frontier Pipeline LLC, a Delaware
limited liability company (“Frontier Pipeline”), Frontier Refining & Marketing LLC, a Delaware limited liability company (“FRMC”), and Frontier Refining LLC, a Delaware limited liability company
(collectively with Holly Biofuels, Ethanol Management, Frontier El Dorado, Frontier Pipeline and FRMC, the “Guaranteeing Subsidiaries”), each a subsidiary of HollyFrontier Corporation (or its permitted successor), a Delaware
corporation (the “Company”), the Company, the other Guarantors (as defined in the Indenture referred to herein) and U.S. Bank Trust National Association, as trustee under the Indenture referred to below (the
“Trustee”). 
 W I T N E S S E T H 
 WHEREAS, the Company has heretofore executed and delivered to the Trustee an indenture (the “Indenture”), dated as of June 10, 2009, providing for the issuance of 9.875% Senior Notes
due 2017 (the “Notes”), as supplemented by the First Supplemental Indenture, dated as of June 14, 2011; 

WHEREAS, the Indenture provides that under certain circumstances the Guaranteeing Subsidiaries shall execute and deliver to the Trustee a
supplemental indenture pursuant to which the Guaranteeing Subsidiaries shall unconditionally guarantee all of the Company’s Obligations under the Notes and the Indenture on the terms and conditions set forth herein (the “Subsidiary
Guarantee”); and 
 WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and
deliver this Second Supplemental Indenture. 
 NOW, THEREFORE, in consideration of the foregoing and for other good and valuable
consideration, the receipt of which is hereby acknowledged, the Guaranteeing Subsidiaries and the Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes as follows: 

1. CAPITALIZED TERMS. Capitalized terms used herein without definition shall have the meanings assigned to
them in the Indenture. 
 2. AGREEMENT TO GUARANTEE. The Guaranteeing Subsidiaries
hereby agree to provide an unconditional guarantee on the terms and subject to the conditions set forth in the Subsidiary Guarantee and in the Indenture including but not limited to Article 10 thereof. 

3. NO RECOURSE AGAINST OTHERS. No director, officer, employee, incorporator,
or owner of an Equity Interest of the Company or any Guarantor, as such, will have any liability for any obligations of the Company or the Guarantors under the Notes, this Second Supplemental Indenture or the Subsidiary Guarantee or for any claim
based on, in respect of, or by reason of, such obligations or their creation. Each Holder of the Notes by accepting a Note waives and releases all such liability. The waiver and release are part of the consideration for issuance of the Notes.


  
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 4. NEW YORK LAW TO GOVERN. THE LAW OF THE STATE OF NEW YORK SHALL GOVERN AND BE USED TO
CONSTRUE THIS SECOND SUPPPLEMENTAL INDENTURE. 
 5. COUNTERPARTS. The parties may sign any number of copies of
this Second Supplemental Indenture. Each signed copy shall be an original, but all of them together represent the same agreement. 
 6. EFFECT OF HEADINGS. The Section headings herein are for convenience only and shall not affect the construction hereof. 

7. THE TRUSTEE. The Trustee shall not be responsible in any manner whatsoever for or in respect of the
validity or sufficiency of this Second Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by the Guaranteeing Subsidiaries and the Company. 

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

			
	 GUARANTEEING SUBSIDIARIES:
  

HOLLY BIOFUELS LLC

		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	ETHANOL MANAGEMENT COMPANY LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	FRONTIER EL DORADO REFINING LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	FRONTIER PIPELINE LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	FRONTIER REFINING & MARKETING LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	FRONTIER REFINING LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer



  
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	 COMPANY:
  

HOLLYFRONTIER CORPORATION

		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	 EXISTING GUARANTORS:

 
 EAGLE CONSOLIDATION LLC

		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLY TRANSPORTATION LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLY REFINING & MARKETING – TULSA LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	BLACK EAGLE LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLYFRONTIER PAYROLL SERVICES, INC.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer



  
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	HOLLY PETROLEUM, INC.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLYFRONTIER REFINING & MARKETING LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLY REFINING & MARKETING COMPANY — WOODS CROSS LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLY REFINING COMMUNICATIONS, INC.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLY UNEV PIPELINE COMPANY
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLY WESTERN ASPHALT COMPANY
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer



  
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	LEA REFINING COMPANY
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	NAVAJO HOLDINGS, INC.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	NAVAJO PIPELINE GP, L.L.C.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	NAVAJO PIPELINE LP, L.L.C.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	 NAVAJO PIPELINE CO., L.P.
  

By: Navajo Pipeline GP, L.L.C., its general partner

		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	NAVAJO REFINING COMPANY, L.L.C.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer



  
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	NAVAJO REFINING GP, L.L.C.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	NAVAJO WESTERN ASPHALT COMPANY
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	NK ASPHALT PARTNERS
	
	By:    Navajo Western Asphalt Company, partner
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	By:    Holly Western Asphalt Company, partner
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLY REALTY, LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer


  

			
	HOLLYMARKS, LLC
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer



  
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	HRM REALTY, L.L.C.
		
	By:	 	/s/    Stephen D. Wise
		 	Name: Stephen D. Wise
		 	Title: Vice President and Treasurer



  
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	TRUSTEE:
	
	 U.S. BANK TRUST NATIONAL ASSOCIATION,
 as Trustee

		
	By:	 	/s/    Steven A. Finklea
		 	Name: Steven A. Finklea, CCTS
		 	Title: Vice President



  
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