Document:

Exhibit 4.9

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]

 

2

 

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	 	 

 

S-1

 

	 	 	 	 	 	 	 	 	 	 	 
	 	 	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	 	 

 

S-2

 

	 	 	 	 	 	 	 	 	 	 	 
	 	 	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	 	 

 

S-3

 

	 	 	 	 	 	 	 	 	 	 	 
	 	 	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	 	 

 

S-4

 

	 	 	 	 	 	 	 	 	 	 	 
	 	 	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	 	 

 

S-5

 

	 	 	 	 	 	 	 	 	 	 	 
	 	 	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	 	 

 

S-6

 

	 	 	 	 	 
	 	U.S. BANK NATIONAL ASSOCIATION,

as Trustee

 	 
	 	By:  	 	 
	 	 	Seth Dodson 	 
	 	 	Vice President 	 
	 

 

S-7Exhibit 10.41

Exhibit 10.41

THIRD AMENDMENT TO THE

HOLLY ENERGY PARTNERS, L.P.

LONG-TERM INCENTIVE PLAN

THIS THIRD AMENDMENT is effective March 3, 2009 (the “Effective Date”) and is made by Holly
Logistic Services, L.L.C., a Delaware limited liability company (the “Company”).

W I T N E S S E T H:

WHEREAS, the board of directors of the Company (the “Board”) adopted the Holly Energy
Partners, L.P. Long-Term Incentive Plan, effective August 4, 2004 (the “Plan”);

WHEREAS, Section 7(a) of the Plan provides that the Plan may be amended by the Compensation
Committee of the Board (the “Committee”) without approval of any unitholder of the Company or
approval of any other person, except as required by the rules of the securities exchange on which
the units are traded, or except as to provide for a change that materially reduces the benefits of
a participant; and

WHEREAS, the Committee has determined that it is desirable to amend the Plan to provide for
the grant of unrestricted unit awards under the Plan.

NOW, THEREFORE, the Plan shall be amended as of the Effective Date as set forth below:

1. The definition of “Award” in Section 2 of the Plan is hereby deleted in its entirety and
replaced with the following:

“Award” means an Option, Restricted Unit, Phantom Unit, Unit Appreciation Right
or Unit Award granted under the Plan, and shall include any tandem DERs granted with
respect to a Phantom Unit.

2. The following definition shall be added to the end of Section 2 of the Plan:

“Unit Award” means a grant of a Unit that is not subject to a Restricted
Period.

3. Section 6(d) of the Plan shall become Section 6(e) and a new Section 6(d) shall be added to
the Plan to read as follows:

(d) Unit Awards. Unit Awards may be granted under the Plan to such Employees,
Consultants and/or Directors and in such amounts as the Committee, in its
discretion, may select.

NOW, THEREFORE, be it further provided that, except as set forth above, the Plan shall
continue to read in its current state.

 

 

 

IN WITNESS WHEREOF, the Company has caused the execution of this Third Amendment by its duly
authorized officer, effective as of the Effective Date.

	 	 	 	 	 
	 	HOLLY LOGISTIC SERVICES, L.L.C.

 	 
	 	By:  	 	 
	 	 	Matthew P. Clifton 	 
	 	 	Chief Executive Officer

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