exv4w1






Exhibit 4.1




THIRD SUPPLEMENTAL INDENTURE




     Third Supplemental Indenture (this “Third Supplemental Indenture”), dated as of June
11, 2009, among Lovington-Artesia, L.L.C., a Delaware limited liability company (the “Guaranteeing
Subsidiary”), Holly Energy Partners, L.P., a Delaware limited partnership (“Holly Energy
Partners”), and Holly Energy Finance Corp. (“Finance Corp.” and, together with Holly Energy
Partners, the “Issuers”), the other Guarantors (as defined in the Indenture referred to below) and
U.S. Bank National Association, as trustee under the Indenture referred to below (the “Trustee”).



W I T N E S S E T H




     WHEREAS, the Issuers have heretofore executed and delivered to the Trustee an indenture (the
“Indenture”), dated as of February 28, 2005 providing for the issuance of 61/4% Senior Notes due 2015
(the “Notes”), a First Supplemental Indenture, dated as of March 10, 2005, providing for the
addition of HEP Fin-Tex/Trust River, L.P., a Texas limited partnership, as a Guarantor under the
Indenture, and a Second Supplemental Indenture, dated as of April 27, 2005, providing for the
correction of the redemption prices tables in the Indenture and the form of Note;



     WHEREAS, the Indenture provides that under certain circumstances the Guaranteeing Subsidiary
shall execute and deliver to the Trustee a supplemental indenture pursuant to which the
Guaranteeing Subsidiary shall unconditionally guarantee all of the Issuers’ Obligations under the
Notes and the Indenture on the terms and conditions set forth herein (the “Note Guarantee”); and



     WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and
deliver this Third 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 Subsidiary 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 Subsidiary hereby agrees to provide an
unconditional Guarantee on the terms and subject to the conditions set forth in the Note Guarantee
and in the Indenture including but not limited to Article 10 thereof.



     4. No Recourse Against Others. No past, present or future director, officer,
employee, incorporator, stockholder or agent of the Guaranteeing Subsidiary, as such, shall have
any liability for any obligations of the Issuers or any Guaranteeing Subsidiary under the Notes,
any Note Guarantees, the Indenture or this Third Supplemental Indenture 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. Such waiver may not be effective to waive liabilities



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under the federal securities laws and it is the view of the SEC that such a waiver is against
public policy.




     5. NEW YORK LAW TO GOVERN. THE LAW OF THE STATE OF NEW YORK SHALL GOVERN AND BE USED TO
CONSTRUE THIS THIRD SUPPPLEMENTAL INDENTURE.



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



     7. Effect of Headings. The Section headings herein are for convenience only and
shall not affect the construction hereof.



     8. The Trustee. The Trustee shall not be responsible in any manner whatsoever for or
in respect of the validity or sufficiency of this Third Supplemental Indenture or for or in respect
of the recitals contained herein, all of which recitals are made solely by the Guaranteeing
Subsidiary and the Issuers.



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



	 	 	 	 	 	 	 	 	 	 	 
	 	 	GUARANTEEING SUBSIDIARY:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	LOVINGTON-ARTESIA, L.L.C.,	 	 
	 	 	a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	Holly Energy Partners — Operating, L.P.,	 	 
	 	 	 	 	a Delaware limited partnership,	 	 
	 	 	 	 	its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics GP, L.L.C., a Delaware limited
liability company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C., a Delaware
limited liability company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 

Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	 	 	Senior Vice President and	 	 
	 

	 	 	 	 	 	 	 	Chief Financial Officer	 	 






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	 	 	ISSUERS:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HOLLY ENERGY PARTNERS, L.P.	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	HEP Logistic Holdings, L.P.,	 	 
	 	 	 	 	its general partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C.,	 	 
	 	 	 	 	 	 	its general partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 

Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	 	 	Senior Vice President and	 	 
	 

	 	 	 	 	 	 	 	Chief Financial Officer	 	 






	 	 	 	 	 
	 	HOLLY ENERGY FINANCE CORP.

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Bruce R. Shaw 	 
	 	 	Vice President and Chief Financial Officer	 
	 



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	 	 	OTHER GUARANTORS:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HEP LOGISTICS GP, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	Holly Energy Partners, L.P., a Delaware limited
partnership, its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C., a Delaware
limited liability company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw
 

Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	 	 	Senior Vice President and

Chief Financial Officer	 	 






	 	 	 	 	 	 	 	 	 	 	 
	 	 	HOLLY ENERGY PARTNERS-OPERATING, L.P., a Delaware limited
partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	HEP Logistics GP, L.L.C., a Delaware limited liability
company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C., a Delaware
limited liability company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw
 

Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	 	 	Senior Vice President and

Chief Financial Officer	 	 











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	 	HEP PIPELINE GP, L.L.C., a Delaware limited liability
company
	 
	 	 
	 

	 	HEP REFINING GP, L.L.C., a Delaware limited liability
company
	 
	 	 
	 

	 	HEP MOUNTAIN HOME, L.L.C., a Delaware limited liability
company
	 
	 	 
	 

	 	HEP PIPELINE, L.L.C., a Delaware limited liability
company
	 
	 	 
	 

	 	HEP REFINING, L.L.C., a Delaware limited liability
company
	 
	 	 
	 

	 	HEP WOODS CROSS, L.L.C., a Delaware limited liability
company






	 	 	 	 	 	 	 	 	 	 	 
	 	 	 Each by:	 	Holly Energy Partners—Operating, L.P., a
	 	 	 	 	Delaware limited partnership and its Sole Member
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics GP, L.L.C., a Delaware
limited liability company, its General
Partner
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole Member
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General Partner
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C., a
Delaware limited liability company, its
General Partner
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw
 

Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	 	 	Senior Vice President and
Chief Financial Officer	 	 





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	 	HEP FIN-TEX/TRUST RIVER, L.P., a Texas limited
partnership
	 
	 	 
	 

	 	HEP NAVAJO SOUTHERN, L.P., a Delaware limited partnership
	 
	 	 
	 

	 	HEP PIPELINE ASSETS, LIMITED PARTNERSHIP, a Delaware

limited partnership






	 	 	 	 	 	 	 	 	 	 	 
	 	 	 Each by:	 	HEP Pipeline GP, L.L.C., a Delaware limited liability
company and its General Partner
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Energy Partners—Operating, L.P., a
Delaware limited partnership, its Sole
Member
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics GP, L.L.C., a Delaware
limited liability company, its General
Partner
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole Member
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General Partner
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C., a
Delaware limited liability company, its
General Partner
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw
 

Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	 	 	Senior Vice President and	 	 
	 

	 	 	 	 	 	 	 	Chief Financial Officer	 	 





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	 	 	HEP REFINING ASSETS, L.P., a Delaware limited partnership	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	HEP Refining GP, L.L.C., a Delaware limited liability
company and its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Energy Partners—Operating, L.P., a
Delaware limited partnership, its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics GP, L.L.C., a Delaware limited
liability company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	Holly Logistic Services, L.L.C., a Delaware
limited liability company, its General Partner	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 

Bruce R. Shaw
	 	 
	 

	 	 	 	 	 	 	 	Senior Vice President and	 	 
	 

	 	 	 	 	 	 	 	Chief Financial Officer	 	 






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U.S. BANK NATIONAL ASSOCIATION,

as Trustee

 	 
	 	By:  	/s/ Seth Dodson
 	 
	 	 	Seth Dodson 	 
	 	 	Vice President 	 
	 




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