Exhibit 4.1
 HOLLYFRONTIER CORPORATION
(successor-in-interest to Frontier Oil Corporation),
 as Issuer,
 THE GUARANTORS NAMED HEREIN
 and
 WELLS FARGO BANK, NATIONAL ASSOCIATION,
 as Trustee
 THIRD SUPPLEMENTAL INDENTURE
 dated as of July 1, 2011
 to Indenture dated as of November 22, 2010
 Providing for Issuance of
 67⁄8% Senior Notes due 2018




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THIRD SUPPLEMENTAL INDENTURE
 Third Supplemental Indenture Company Trustee Indenture
 FOC Merger Sub Merger
   Guarantee
 ECLLC
 HFRMLLC
   1




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2




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Issuer:
HOLLYFRONTIER CORPORATIONBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President & Chief Executive OfficerGuarantors:
FRONTIER REFINING & MARKETING LLC
FRONTIER REFINING LLC
FRONTIER EL DORADO REFINING LLC
FRONTIER PIPELINE LLC
ETHANOL MANAGEMENT COMPANY LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    PresidentBLACK EAGLE LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerEAGLE CONSOLIDATION LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY BIOFUELS LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer 3




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HOLLYFRONTIER PAYROLL SERVICES, INC.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY PETROLEUM, INC.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY REALTY, LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLYFRONTIER REFINING & MARKETING LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY REFINING & MARKETING  TULSA LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY REFINING & MARKETING 
WOODS CROSS LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer 4




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HOLLY REFINING COMMUNICATIONS INC.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY TRANSPORTATION LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY UNEV PIPELINE COMPANYBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY WESTERN ASPHALT COMPANYBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLYMARKS, LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHRM REALTY, LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer 5




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LEA REFINING COMPANYBy:

/s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO HOLDINGS, INC.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO PIPELINE CO., L.P.By:
    Navajo Pipeline G.P., L.L.C.Its General PartnerBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO PIPELINE GP, L.L.C.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO PIPELINE LP, L.L.C.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO REFINING COMPANY, L.L.C.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer 6




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NAVAJO REFINING GP, L.L.C.By:

/s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO WESTERN ASPHALT COMPANYBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNK ASPHALT PARTNERS,
DBA HOLLY ASPHALT COMPANY HOLLY WESTERN ASPHALT COMPANY,
PARTNERBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO WESTERN ASPHALT COMPANY,
PARTNERBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer Trustee:
WELLS FARGO BANK, N.A., as TrusteeBy:

/s/ Patrick T. GiordanoName:
    Patrick T. GiordanoTitle:
    Vice President 7




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Guarantors:
BLACK EAGLE LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerEAGLE CONSOLIDATION LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY BIOFUELS LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLYFRONTIER PAYROLL SERVICES, INC.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY PETROLEUM, INC.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer




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HOLLY REALTY, LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLYFRONTIER REFINING & MARKETING LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY REFINING & MARKETING  TULSA LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY REFINING & MARKETING -
WOODS CROSS LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY REFINING COMMUNICATIONS INC.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY TRANSPORTATION LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer




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HOLLY UNEV PIPELINE COMPANYBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLY WESTERN ASPHALT COMPANYBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHOLLYMARKS, LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerHRM REALTY, LLCBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerLEA REFINING COMPANYBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO HOLDINGS, INC.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer




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NAVAJO PIPELINE CO., L.P.By:
    Navajo Pipeline G.P., L.L.C.Its General PartnerBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO PIPELINE GP, L.L.C.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO PIPELINE LP, L.L.C.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO REFINING COMPANY, L.L.C.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO REFINING GP, L.L.C.By:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO WESTERN ASPHALT COMPANYBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer




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NK ASPHALT PARTNERS,
DBA HOLLY ASPHALT COMPANYHOLLY WESTERN ASPHALT COMPANY,
PARTNERBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive OfficerNAVAJO WESTERN ASPHALT COMPANY,
PARTNERBy:
    /s/ Michael C. JenningsName:
    Michael C. JenningsTitle:
    President and Chief Executive Officer