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EXHIBIT 4.6




SECOND SUPPLEMENTAL INDENTURE




     Second Supplemental Indenture (this “Second Supplemental Indenture”), dated as
of April 27, 2005, among Holly Energy Partners, L.P., a Delaware limited partnership (“Holly Energy
Partners”), Holly Energy Finance Corp., a Delaware corporation (“Finance Corp.” and, together with
Holly Energy Partners, the “Issuers”), the 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 6 1/4% Senior Notes
due 2015 (the “Notes”), and 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;



     WHEREAS, Section 9.01(1) of the Indenture authorizes the Issuers, the Guarantors and the
Trustee to amend or supplement the Indenture or the Notes or the Note Guarantees, without the
consent of any Holder of the Notes, to cure any ambiguity, defect or inconsistency;



     WHEREAS, Section 9.01(6) of the Indenture authorizes the Issuers, the Guarantors and the
Trustee to amend or supplement the Indenture or the Notes or the Note Guarantees, without the
consent of any Holder of the Notes, to conform the text of the Indenture or the Note Guarantees to
the Issuers’ Offering Memorandum to the extent that such provision was intended to be a verbatim
recitation of a provision of the Indenture or the Note Guarantees;



     WHEREAS, the reference to “102.833%” in the redemption prices table in Section 3.07(c) of the
Indenture and Paragraph 5(a) of the form of Note with respect to the twelve-month period beginning
March 1, 2011 is defective;



     WHEREAS, the reference to “102.083%” in the redemption prices table under the section
captioned “Optional Redemption” in the Offering Memorandum with respect to the twelve-month period
beginning March 1, 2011 is correct;



     WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and
deliver this Second Supplemental Indenture; and



     WHEREAS, all conditions and requirements necessary to make this Second Supplemental Indenture
a valid, legal, binding and enforceable instrument in accordance with its terms have been performed
and fulfilled by the parties hereto, and the execution and delivery thereof have been in all
respects duly authorized by the parties hereto.



     NOW, THEREFORE, in consideration of the foregoing and for other good and valuable
consideration, the receipt of which is hereby acknowledged, each party hereby agrees, for the
benefit of the others and for the equal and ratable benefit of the Holders of the Notes as follows:



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     1. Capitalized Terms. Capitalized terms used herein without definition shall have
the meanings assigned to them in the Indenture.



     2. Amendments to Indenture.




     a. Section 3.07(c) of the Indenture is hereby amended by changing the reference to
“102.833%” in the redemption prices table with respect to the twelve-month period beginning
March 1, 2011 to “102.083%”.




     b. Paragraph 5(a) of the form of Note included as Exhibit A to the Indenture is hereby
amended by changing the reference to “102.833%” in the redemption prices table with respect
to the twelve-month period beginning March 1, 2011 to “102.083%”.



     3. Ratification. This Second Supplemental Indenture is executed and shall be
construed as a supplement to the Indenture and, as provided in the Indenture, this Second
Supplemental Indenture forms a part of the Indenture. Except to the extent amended by or
supplemented by this Second Supplemental Indenture, the Issuers, the Guarantors and the Trustee
hereby ratify, confirm and reaffirm the Indenture in all respects.



     4. NEW YORK LAW TO GOVERN. THE LAW OF THE STATE OF NEW YORK SHALL GOVERN AND BE USED TO
CONSTRUE THIS SECOND SUPPLEMENTAL 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 Issuers.



[Signature Pages Follow]




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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.



	 	 	 	 	 	 	 	 	 
	 	 	ISSUERS:
	 
	 	 	 	 	 	 	 	 
	 	 	HOLLY ENERGY PARTNERS, L.P., a Delaware limited
partnership
	 
	 	 	 	 	 	 	 	 
	 	 	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/ Stephen J. McDonnell
	

	 	 	 	 	 	 	 	 
	

	 	 	 	 	 	 	 	Stephen J. McDonnell
	

	 	 	 	 	 	 	 	Vice President and Chief Financial Officer
	 
	 	 	 	 	 	 	 	 
	 	 	HOLLY ENERGY FINANCE CORP., a Delaware corporation
	 
	 	 	 	 	 	 	 	 
	 	 	By:	 	/s/ Stephen J. McDonnell
	 	 	 	 	 
	 	 	 	 	Stephen J. McDonnell
	 	 	 	 	Vice President and Chief Financial Officer






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	 	 	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/ Stephen J. McDonnell
	

	 	 	 	 	 	 	 	 
	

	 	 	 	 	 	 	 	Stephen J. McDonnell
	

	 	 	 	 	 	 	 	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/ Stephen J. McDonnell
	

	 	 	 	 	 	 	 	 
	

	 	 	 	 	 	 	 	Stephen J. McDonnell
	

	 	 	 	 	 	 	 	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/ Stephen J. McDonnell
	

	 	 	 	 	 	 	 	 
	

	 	 	 	 	 	 	 	Stephen J. McDonnell
	

	 	 	 	 	 	 	 	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/ Stephen J. McDonnell
	

	 	 	 	 	 	 	 	 
	

	 	 	 	 	 	 	 	Stephen J. McDonnell
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/ Stephen J. McDonnell
	

	 	 	 	 	 	 	 	 
	

	 	 	 	 	 	 	 	Stephen J. McDonnell
	

	 	 	 	 	 	 	 	Vice President and Chief Financial Officer






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	 	U.S. BANK NATIONAL ASSOCIATION,

as Trustee

 	 
	 	By:  	/s/ Adam M. Dalmy
 	 
	 	 	Adam M. Dalmy 	 
	 	 	Vice President 	 
	 




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