Exhibit 4.1
 THIRD SUPPLEMENTAL INDENTURE
 Third Supplemental Indenture Third Supplemental Indenture Guaranteeing
Subsidiary Holly Energy
Partners Finance Corp. Issuers Trustee
  Indenture 1 4 Notes
 Note Guarantee
   Capitalized Terms
 Agreement to Guarantee
 No Recourse Against Others
 1




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Counterparts
 Effect of Headings
 The Trustee
 2




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GUARANTEEING SUBSIDIARY:LOVINGTON-ARTESIA, L.L.C.,a Delaware limited liability companyBy:
    
    Holly Energy Partners  Operating, L.P.,a Delaware limited partnership,its Sole MemberBy:
    
    HEP Logistics GP, L.L.C., a Delaware limited
liability company, its General PartnerBy:
    
    Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole MemberBy:
    
    HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General PartnerBy:
    
    Holly Logistic Services, L.L.C., a Delaware
limited liability company, its General PartnerBy:
    
    /s/ Bruce R. ShawBruce R. ShawSenior Vice President andChief Financial Officer
 S-1




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ISSUERS:HOLLY ENERGY PARTNERS, L.P.By:
    
    HEP Logistic Holdings, L.P.,its general partnerBy:
    
    Holly Logistic Services, L.L.C.,its general partnerBy:
    
    /s/ Bruce R. ShawBruce R. ShawSenior Vice President andChief Financial Officer
 HOLLY ENERGY FINANCE CORP.By:
    /s/ Bruce R. ShawBruce R. ShawVice President and Chief Financial Officer S-2




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OTHER GUARANTORS:HEP LOGISTICS GP, L.L.C., a Delaware limited liability
companyBy:
    
    Holly Energy Partners, L.P., a Delaware limited
partnership, its Sole MemberBy:
    
    HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General PartnerBy:
    
    Holly Logistic Services, L.L.C., a Delaware
limited liability company, its General PartnerBy:
    
    /s/ Bruce R. Shaw

Bruce R. ShawSenior Vice President and
Chief Financial Officer
 HOLLY ENERGY PARTNERS-OPERATING, L.P., a Delaware limited
partnershipBy:
    
    HEP Logistics GP, L.L.C., a Delaware limited liability
company, its General PartnerBy:
    
    Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole MemberBy:
    
    HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General PartnerBy:
    
    Holly Logistic Services, L.L.C., a Delaware
limited liability company, its General PartnerBy:
    
    /s/ Bruce R. Shaw

Bruce R. ShawSenior Vice President and
Chief Financial Officer
 
 S-3




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HEP PIPELINE GP, L.L.C., a Delaware limited liability
companyHEP REFINING GP, L.L.C., a Delaware limited liability
companyHEP MOUNTAIN HOME, L.L.C., a Delaware limited liability
companyHEP PIPELINE, L.L.C., a Delaware limited liability
companyHEP REFINING, L.L.C., a Delaware limited liability
companyHEP WOODS CROSS, L.L.C., a Delaware limited liability
company
 Each by:
    
    Holly Energy PartnersOperating, L.P., aDelaware limited partnership and its Sole MemberBy:
    
    HEP Logistics GP, L.L.C., a Delaware
limited liability company, its General
PartnerBy:
    
    Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole MemberBy:
    
    HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General PartnerBy:
    
    Holly Logistic Services, L.L.C., a
Delaware limited liability company, its
General PartnerBy:
    
    /s/ Bruce R. Shaw

Bruce R. ShawSenior Vice President and
Chief Financial Officer
 S-4




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HEP FIN-TEX/TRUST RIVER, L.P., a Texas limited
partnershipHEP NAVAJO SOUTHERN, L.P., a Delaware limited partnershipHEP PIPELINE ASSETS, LIMITED PARTNERSHIP, a Delaware
limited partnership
 Each by:
    
    HEP Pipeline GP, L.L.C., a Delaware limited liability
company and its General PartnerBy:
    
    Holly Energy PartnersOperating, L.P., a
Delaware limited partnership, its Sole
MemberBy:
    
    HEP Logistics GP, L.L.C., a Delaware
limited liability company, its General
PartnerBy:
    
    Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole MemberBy:
    
    HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General PartnerBy:
    
    Holly Logistic Services, L.L.C., a
Delaware limited liability company, its
General PartnerBy:
    
    /s/ Bruce R. Shaw

Bruce R. ShawSenior Vice President andChief Financial Officer
 S-5




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HEP REFINING ASSETS, L.P., a Delaware limited partnershipBy:
    
    HEP Refining GP, L.L.C., a Delaware limited liability
company and its General PartnerBy:
    
    Holly Energy PartnersOperating, L.P., a
Delaware limited partnership, its Sole MemberBy:
    
    HEP Logistics GP, L.L.C., a Delaware limited
liability company, its General PartnerBy:
    
    Holly Energy Partners, L.P., a Delaware
limited partnership, its Sole MemberBy:
    
    HEP Logistics Holdings, L.P., a Delaware
limited partnership, its General PartnerBy:
    
    Holly Logistic Services, L.L.C., a Delaware
limited liability company, its General PartnerBy:
    
    /s/ Bruce R. ShawBruce R. ShawSenior Vice President andChief Financial Officer
 S-6




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U.S. BANK NATIONAL ASSOCIATION,
as TrusteeBy:
    /s/ Seth DodsonSeth DodsonVice President S-7