Document:

Exhibit

Exhibit 4.1

SECOND SUPPLEMENTAL INDENTURE
SECOND SUPPLEMENTAL INDENTURE (this “Second Supplemental Indenture”), dated as of July 26, 2017, among Holly Energy Holdings LLC, a Delaware limited liability company, HEP Cheyenne Shortline LLC, a Delaware limited liability company (the “Guaranteeing Subsidiaries”), Holly Energy Partners, L.P., a Delaware limited partnership (“Holly Energy Partners”), and Holly Energy Finance Corp. (“Finance Corp.” and collectively with Holly Energy Partners, the “Issuers”), the other Guarantors (as defined in the Indenture referred to herein) and U.S. Bank National Association, as trustee under the Indenture referred to herein (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 July 19, 2016, providing for the issuance of 6% Senior Notes due 2024 (the “Notes”) and a First Supplemental Indenture dated as of November 2, 2016, providing for the addition of Woods Cross Operating LLC, a Delaware limited liability company, as 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 Second Supplemental Indenture.
NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the receipt of which is hereby acknowledged, each 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.  Each 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 Subsidiaries, as such, shall have any liability for any obligations of the Issuers or any Guaranteeing Subsidiaries under the Notes, any Note Guarantees, the Indenture or this Second 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 

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the federal securities laws and it is the view of the U.S. Securities and Exchange Commission 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 FIRST 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 each Guaranteeing Subsidiary and the Issuers.

[Remainder of Page Intentionally Left Blank]

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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 SUBSIDIARIES:
HOLLY ENERGY HOLDINGS LLC, a Delaware limited liability company

By:  /s/ John Harrison                                                                       
John Harrison
Vice President and Treasurer

HEP CHEYENNE SHORTLINE LLC, a Delaware limited liability company

By:  /s/ John Harrison                                                               
John Harrison
Vice President and Treasurer

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/ John Harrison             
John Harrison
Vice President and Treasurer

HOLLY ENERGY FINANCE CORP.

By:  /s/ John Harrison             
John Harrison
Vice President and Treasurer

S-2

OTHER GUARANTORS:
EL DORADO OPERATING LLC, a Delaware limited liability company

HEP CASPER SLC LLC, a Delaware limited liability company

HEP CHEYENNE LLC, a Delaware limited liability company

HEP EL DORADO LLC, a Delaware limited liability company

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

HOLLY ENERGY PARTNERS-OPERATING, L.P., a Delaware limited partnership

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

CHEYENNE LOGISTICS LLC, a Delaware limited liability company

EL DORADO LOGISTICS LLC, a Delaware limited liability company

EL DORADO OSAGE LLC, a Delaware limited liability company

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

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

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

HEP TULSA LLC, a Delaware limited liability company

S-3

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

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

HEP SLC, LLC, a Delaware limited liability company

HEP UNEV HOLDINGS LLC, a Delaware limited liability company

HEP UNEV PIPELINE LLC, a Delaware limited liability company

WOODS CROSS OPERATING LLC, 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 WOODS CROSS, L.L.C., a Delaware limited liability company

By:  /s/ John Harrison             
John Harrison
Vice President and Treasurer

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/ John Harrison             
John Harrison
Vice President and Treasurer

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:  /s/ John Harrison             
John Harrison
Vice President and Treasurer

S-6

U.S. BANK NATIONAL ASSOCIATION, 
as Trustee
By:    /s/ Brad Hounsel    
Name:    Brad Hounsel
Title:    Vice President

S-7Exhibit

Exhibit 10.4

HOLLY ENERGY PARTNERS, L.P.
Common Units Representing Limited Partner Interests
having an aggregate offering price of up to
$200,000,000
Amendment to Equity Distribution Agreement
July 28, 2017
Citigroup Global Markets Inc.
388 Greenwich Street
New York, New York 10013

Goldman Sachs & Co. LLC
200 West Street
New York, New York 10282

Merrill Lynch, Pierce, Fenner & Smith  
             Incorporated
One Bryant Park
New York, New York 10036

Ladies and Gentlemen:
THIS AMENDMENT TO EQUITY DISTRIBUTION AGREEMENT (the “Amendment”), is made and entered into as of July 28, 2017, by and among Holly Energy Partners, L.P., a Delaware limited partnership (the “Partnership”), HEP Logistics Holdings, L.P., a Delaware limited partnership (the “General Partner”), Holly Logistic Services, L.L.C., a Delaware limited liability company (the “GP L.L.C.”), and Citigroup Global Markets Inc., Goldman Sachs & Co. LLC and Merrill Lynch, Pierce, Fenner & Smith Incorporated (the “Managers”). The Partnership, the General Partner and the GP L.L.C. are herein referred to as the “HEP Parties.” Capitalized terms used but not otherwise defined herein shall have the respective meanings ascribed to them in the Equity Distribution Agreement (as defined below).
WHEREAS, each of the HEP Parties and the Managers are parties to an Equity Distribution Agreement, dated May 10, 2016, as amended (the “Equity Distribution Agreement”), with respect to the offering and sale of up to $200,000,000 of Common Units;
WHEREAS, each of the HEP Parties and the Managers, by executing this agreement, hereby consent to the amendment of the Equity Distribution Agreement, on the terms and conditions set forth herein.

NOW, THEREFORE, in consideration of the mutual covenants and promises contained herein and for other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, each of the HEP Parties and the Managers agree as follows:
SECTION 1.Amendments to Equity Distribution Agreement. 
(a)    Section 3(f) of the Equity Distribution Agreement is hereby amended and restated in its entirety as follows:
“Notwithstanding any other provision of this Agreement the Partnership shall not request the sale of any Offered Units that would be sold, and the Managers shall not be obligated to sell, (i) during any period in which the Partnership is, or could be deemed to be, in possession of material non-public information or (ii) at any time during the period commencing on the 10th Business Day prior to the time the Partnership issues a press release containing, or shall otherwise publicly announce, its earnings or revenues for a fiscal period or periods (each, an “Earnings Announcement”) through the close of business on the trading day after the date on which the Partnership’s next subsequent Annual Report on Form 10-K or Quarterly Report on Form 10-Q, as the case may be, that includes consolidated financial statements as of and for the same fiscal period or periods, as the case may be, covered by such Earnings Announcement is filed with the Commission.”

(b)    Schedule II of the Equity Distribution Agreement is hereby amended and replaced with Exhibit A hereto. 

SECTION 2.Representations and Warranties.  Each of the HEP Parties, jointly and severally, represents and warrants to, and agrees with the Managers as set forth below in this Section 2.    
(a)Each of the HEP Parties that is a party to this Amendment has all requisite power and authority to execute and deliver this Amendment and perform its respective obligations hereunder.  The Partnership has all requisite limited partnership power and authority to offer, sell and deliver the Common Units in accordance with and upon the terms and conditions set forth in the Equity Distribution Agreement, the Partnership Agreement, the Registration Statement, the Disclosure Package and the Prospectus.  At each Representation Date and each Settlement Date, all limited partner and limited liability company action, as the case may be, required to be taken by any of the HEP Parties or any of their members or partners for the authorization, offering, sale and delivery of the Common Units and the consummation of the transactions contemplated by the Equity Distribution Agreement shall have been validly taken.
(b)This Amendment has been duly authorized, executed and delivered by the HEP Parties.

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(c)The representations and warranties of the HEP Parties contained in the Equity Distribution Agreement, as amended by this Amendment, are true and correct on and as of the date hereof with the same effect as if made on the date hereof. 
SECTION 3.Counterparts.  This Amendment may be executed in one or more counterparts, each of which shall be deemed an original, and all of which together shall constitute one and the same instrument.  
SECTION 4.Effect on Agreement.  Except as specifically modified herein, the Equity Distribution Agreement shall continue to be in full force and effect.  The execution and delivery of this Amendment shall not, except as expressly provided herein, operate as a waiver of any right, power or remedy of any party thereto.  From and after the date hereof, all references in the Equity Distribution Agreement to the “Agreement” shall mean the Equity Distribution Agreement as modified by this Amendment.
SECTION 5.Severability.  Any term or provision of this Amendment that is invalid or unenforceable in any situation in any jurisdiction shall not affect the validity or enforceability of the remaining terms and provisions hereof or the validity or enforceability of the offending term or provision in any other situation or in any other jurisdiction.
SECTION 6.Further Assurances.  Each party to this Amendment shall execute and deliver such documents and shall take such actions as may be reasonably necessary or desirable to effect the transactions described in this Amendment.  
SECTION 7.Governing Law.  THIS AMENDMENT AND ANY CLAIM, CONTROVERSY OR DISPUTE ARISING UNDER OR RELATED THERETO IS GOVERNED BY THE LAW OF THE STATE OF NEW YORK WITHOUT REGARD TO THE CONFLICTS OF LAWS PROVISIONS THEREOF THAT WOULD APPLY THE LAWS OF ANY OTHER STATE.  THE HEP PARTIES AND THE MANAGERS EACH WAIVE TRIAL BY JURY IN ANY ACTION, PROCEEDING OR COUNTERCLAIM BROUGHT BY OR ON BEHALF OF EITHER PARTY WITH RESPECT TO ANY MATTER WHATSOEVER RELATING TO OR ARISING OUT OF THE TERMS OF THIS AMENDMENT AND THE OFFERING CONTEMPLATED HEREBY.
(a) [Signature pages follow]

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If the foregoing is in accordance with your understanding of our agreement, please sign and return to us the enclosed duplicate hereof, whereupon this letter and your acceptance shall represent a binding agreement among the HEP Parties and the Managers.
Very truly yours,

HOLLY ENERGY PARTNERS, L.P.
By:  HEP Logistics Holdings, L.P., its general partner
By:  Holly Logistic Services L.L.C., its general partner
		
	By:
	 /s/ Richard L. Voliva III              
Name:   Richard L. Voliva III 
Title:     Executive Vice President and 

Chief Financial Officer 
HEP LOGISTICS HOLDINGS, L.P.
By:  Holly Logistic Services L.L.C., its general partner
		
	By:
	 /s/ Richard L. Voliva III              
Name:   Richard L. Voliva III 
Title:     Executive Vice President and 

Chief Financial Officer 
HOLLY LOGISTIC SERVICES L.L.C.
		
	By:
	 /s/ Richard L. Voliva III              
Name:   Richard L. Voliva III 
Title:     Executive Vice President and 

Chief Financial Officer 

Signature Page to Amendment to Equity Distribution Agreement

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The foregoing Amendment is hereby confirmed 
and accepted as of the date first written above.

CITIGROUP GLOBAL MARKETS INC.

By:    /s/ Mark Hobbs     
    Name: Mark Hobbs 
    Title: Managing Director

 
GOLDMAN SACHS & CO. LLC

By:    /s/ Daniel Young             
    Name:  Daniel Young 
    Title:    Managing Director

MERRILL LYNCH, PIERCE, FENNER & SMITH 
                              INCORPORATED

By:    /s/ Alexander Kroner             
    Name: Alexander Kroner 
    Title:  Managing Director

Signature Page to Amendment to Equity Distribution Agreement

EXHIBIT A

	
			
	Subsidiary
	Jurisdiction of Organization
	Equity Holder and % Held by Each

	Cheyenne Logistics LLC
	Delaware
	Holly Energy Holdings LLC (100%)

	El Dorado Logistics LLC
	Delaware
	Holly Energy Holdings LLC (100%)

	El Dorado Operating LLC
	Delaware
	Holly Energy Holdings LLC. (100%)

	El Dorado Osage LLC
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Casper SLC LLC
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Cheyenne LLC
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Cheyenne Shortline LLC
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Fin‐Tex/Trust‐River, L.P.
	Texas
	Holly Energy Holdings LLC (99.999% limited partner)
HEP Pipeline GP, L.L.C. (0.001% general partner)

	HEP Logistics GP, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Mountain Home, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Navajo Southern, L.P.
	Delaware
	Holly Energy Holdings LLC (99.999% limited partner)
HEP Pipeline GP, L.L.C. (0.001% general partner)

	HEP Pipeline, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Pipeline Assets, Limited Partnership
	Delaware
	Holly Energy Holdings LLC (99.999% limited partner)
HEP Pipeline GP, L.L.C. (0.001% general partner)

	HEP Pipeline GP, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Refining, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Refining Assets, L.P.
	Delaware
	Holly Energy Holdings LLC (99.999% limited partner)
HEP Refining GP, L.L.C. (0.001% general partner)

	HEP Refining GP, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP SLC, LLC
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP Tulsa LLC
	Delaware
	Holly Energy Holdings LLC (100%)

	HEP UNEV Holdings LLC
	Delaware
	Holly Energy Partners, L.P. (100% class A units)
HollyFrontier Holdings LLC (100% class B units)

	HEP UNEV Pipeline LLC
	Delaware
	HEP UNEV Holdings (100%)

	HEP Woods Cross, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	Holly Energy Holdings LLC
	Delaware
	Holly Energy Partners, L.P. (100%)

	Holly Energy Storage-Lovington LLC
	Delaware
	HEP Refining, L.L.C. (100%)

	Holly Energy Finance Corp.
	Delaware
	Holly Energy Partners, L.P. (100%)

	Holly Energy Partners—Operating, L.P.
	Delaware
	Holly Energy Partners, L.P. (99.999% limited partner)
HEP Logistics GP, L.L.C. (0.001% general partner)

	Lovington-Artesia, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	Roadrunner Pipeline, L.L.C.
	Delaware
	Holly Energy Holdings LLC (100%)

	Woods Cross Operating LLC
	Delaware
	Holly Energy Holdings LLC (100%)

Exhibit A-1

	
			
	Joint Venture
	Jurisdiction of Organization
	Equity Holder and % Held by Each

	Cheyenne Pipeline LLC
	Texas
	HEP Cheyenne LLC (50%)
Rocky Mountain Pipeline System LLC (50%)

	Frontier Aspen LLC
	Delaware
	Plains Pipeline, L.P. (50%)
HEP Casper SLC LLC (50%)

	Osage Pipe Line Company, LLC
	Delaware
	El Dorado Osage LLC (50%)
CHS McPherson Refinery Inc. (50%)

	SLC Pipeline LLC
	Delaware
	Rocky Mountain Pipeline System LLC (75%) 
HEP SLC, LLC (25%)

	UNEV Pipeline, LLC
	Delaware
	Sinclair Transportation Company (25%)
HEP UNEV Pipeline LLC (75%)

Exhibit A-2

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