Exhibit 4.9

SIXTH SUPPLEMENTAL INDENTURE

Sixth Supplemental Indenture (this “Sixth Supplemental Indenture”), dated as of December 15, 2009, among Roadrunner Pipeline, 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, 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, a Third Supplemental Indenture, dated as of June 11, 2009, providing for the addition of Lovington-Artesia, L.L.C., a Delaware limited liability company, as a Guarantor under the Indenture, a Fourth Supplemental Indenture, dated as of June 29, 2009, providing for the addition of HEP SLC, L.L.C., a Delaware limited liability company, as a Guarantor under the Indenture, and a Fifth Supplemental Indenture dated as of July 13, 2009, providing for the addition of HEP Tulsa LLC, a Delaware limited liability company, as a Guarantor under the Indenture;

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 Sixth 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.

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

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

5. Counterparts. The parties may sign any number of copies of this Sixth 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 Sixth 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.

[Remainder of Page Intentionally Left Blank]

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

		GUARANTEEING SUBSIDIARY:
		ROADRUNNER PIPELINE, 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:
								Bruce R. Shaw
								Senior Vice President and
								Chief Financial Officer

		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:
								Bruce R. Shaw
								Senior Vice President and
								Chief Financial Officer
		HOLLY ENERGY FINANCE CORP.
		By:
				Bruce R. Shaw Vice President and Chief Financial Officer

		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:
								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:
								Bruce R. Shaw Senior Vice President and
								Chief Financial Officer

		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
		LOVINGTON-ARTESIA, L.L.C., a Delaware limited liability company
		HEP SLC, LLC, a Delaware limited liability company
		HEP TULSA LLC, a Delaware limited liability company
		Each 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:
								Bruce R. Shaw
								Senior Vice President and
								Chief Financial Officer

		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, 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:
								Bruce R. Shaw
								Senior Vice President and
								Chief Financial Officer

		HEP REFINING ASSETS, L.P., a Delaware limited partnership
		By:		HEP Refining GP, L.L.C., a Delaware limited liability company, 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:
								Bruce R. Shaw Senior Vice President and
								Chief Financial Officer