Document:

Exhibit 4.1

Exhibit 4.1

SEVENTH SUPPLEMENTAL INDENTURE

Seventh Supplemental Indenture (this “Seventh Supplemental Indenture”), dated as of
April 14, 2010, among Holly Energy Storage-Tulsa LLC, a Delaware limited liability company (“HES
Tulsa”) and Holly Energy Storage-Lovington LLC (“HES Lovington” and collectively with HES Tulsa,
the “Guaranteeing Subsidiaries”), 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, 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, and a Sixth Supplemental Indenture
dated as of December 15, 2009, providing for the addition of Roadrunner Pipeline L.L.C., a Delaware
limited liability company, as a Guarantor under the Indenture;

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 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 Seventh 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.

Seventh Supplemental 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 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 Subsidiaries, as such, shall have
any liability for any obligations of the Issuers or any Guaranteeing Subsidiaries under the Notes,
any Note Guarantee, the Indenture or this Seventh 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 SEVENTH SUPPLEMENTAL INDENTURE.

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

[Remainder of Page Intentionally Left Blank]

Seventh Supplemental Indenture

 

 

 

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

	 	 	 	 	 
	 	GUARANTEEING SUBSIDIARIES:

HOLLY ENERGY STORAGE-TULSA LLC, a Delaware limited
liability company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Senior Vice President and Chief Financial Officer 	 
	 
	 	HOLLY ENERGY STORAGE-LOVINGTON LLC, a Delaware limited
liability company

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

Signature Page to Seventh Supplemental Indenture

 

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:	 	/s/ Bruce R. Shaw	 	 
	 	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Name:
	 	Bruce R. Shaw	 	 
	 

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

Signature Page to Seventh Supplemental Indenture

 

S-2

 

	 	 	 	 	 
	 	OTHER GUARANTORS:

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

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Vice President and Chief Financial Officer 	 
	 
	 	HOLLY ENERGY PARTNERS-OPERATING, L.P., a Delaware limited
partnership

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

Signature Page to Seventh Supplemental Indenture

 

S-3

 

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

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

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

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

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

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

HEP TULSA LLC, a Delaware limited liability company

HEP SLC, LLC, a Delaware limited liability company

LOVINGTON-ARTESIA, L.L.C., a Delaware limited liability
company

ROADRUNNER PIPELINE, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	Each By:	 	Holly Energy Partners – Operating, L.P., a Delaware
limited liability company and Its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	By:	 	/s/ Bruce R. Shaw	 	 
	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Name:
	 	Bruce R. Shaw	 	 
	 

	 	 	 	 	 	Title:
	 	Vice President and Chief Financial Officer	 	 

Signature Page to Seventh Supplemental Indenture

 

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:	 	/s/ Bruce R. Shaw	 	 
	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Name:
	 	Bruce R. Shaw	 	 
	 

	 	 	 	 	 	Title:
	 	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:	 	/s/ Bruce R. Shaw	 	 
	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Name:
	 	Bruce R. Shaw	 	 
	 

	 	 	 	 	 	Title:
	 	Vice President and Chief Financial Officer	 	 

Signature Page to Seventh Supplemental Indenture

 

S-5

 

	 	 	 	 	 
	 	U.S. BANK NATIONAL ASSOCIATION,

as Trustee

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

Signature Page to Seventh Supplemental Indenture

 

S-6Exhibit 4.2

Exhibit 4.2

EIGHTH SUPPLEMENTAL INDENTURE

Eighth Supplemental Indenture (this “Eighth Supplemental Indenture”), dated as of
June 4, 2010, among HEP Operations LLC, 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, 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, a Sixth Supplemental Indenture dated
as of December 15, 2009, providing for the addition of Roadrunner Pipeline L.L.C., a Delaware
limited liability company, as a Guarantor under the Indenture, and a Seventh Supplemental Indenture
dated as of April 14, 2010, providing for the addition of Holly Energy Storage-Tulsa LLC, a
Delaware limited liability company and Holly Energy Storage-Lovington LLC, a Delaware limited
liability company, as Guarantors 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 Eighth 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. 

Eighth Supplemental 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 Guarantee, the Indenture or this Eighth 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 EIGHTH SUPPLEMENTAL INDENTURE.

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

Eighth Supplemental Indenture

 

 

 

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

	 	 	 	 	 	 	 	 	 	 	 
	 	 	GUARANTEEING SUBSIDIARY:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	HEP OPERATIONS LLC, a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	 	 	By:	 	/s/ Bruce R. Shaw	 	 
	 	 	 	 	 	 	 
	 	 	 	 	Name: Bruce R. Shaw	 	 
	 	 	 	 	Title:   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:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

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

Signature Page to Eighth Supplemental Indenture

 

S-1

 

	 	 	 	 	 
	 	OTHER GUARANTORS:

HEP LOGISTICS GP, L.L.C., a Delaware limited liability

company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Vice President and Chief Financial Officer 	 
	 
	 	HOLLY ENERGY PARTNERS-OPERATING, L.P., a Delaware limited
partnership

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Vice President and Chief Financial Officer 	 
	 
	 	HOLLY ENERGY STORAGE-TULSA LLC, a Delaware limited
liability company

 	 
	 	By:  	/s/ Bruce R. Shaw
 	 
	 	 	Name:  	Bruce R. Shaw 	 
	 	 	Title:  	Senior Vice President and Chief Financial
Officer 	 
	 
	 	HOLLY ENERGY STORAGE-LOVINGTON LLC, a Delaware limited
liability company

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

Signature Page to Eighth Supplemental Indenture

 

S-2

 

	 	 	 	 	 	 	 	 	 
	 	 	HEP PIPELINE GP, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP PIPELINE, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP MOUNTAIN HOME, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP REFINING, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP REFINING GP, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP WOODS CROSS, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP TULSA LLC, a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	HEP SLC, LLC, a Delaware limited liability company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	LOVINGTON-ARTESIA, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	ROADRUNNER PIPELINE, L.L.C., a Delaware limited liability
company	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	Each By:	 	Holly Energy Partners – Operating, L.P., a Delaware
limited liability company and Its Sole Member	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	 	 	By:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	Title:   Vice President and Chief Financial Officer	 	 

Signature Page to Eighth Supplemental Indenture

 

S-3

 

	 	 	 	 	 	 	 	 	 
	 	 	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:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	Title:   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:
	 	/s/ Bruce R. Shaw	 	 
	 

	 	 	 	 	 	 	 	 
	 

	 	 	 	 	 	Name: Bruce R. Shaw	 	 
	 

	 	 	 	 	 	Title:   Vice President and Chief Financial Officer	 	 

Signature Page to Eighth Supplemental Indenture

 

S-4

 

	 	 	 	 	 
	 	TRUSTEE:

U.S. BANK NATIONAL ASSOCIATION,

as Trustee

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

Signature Page to Eighth Supplemental Indenture

 

S-5

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