EXHIBIT 3.5

EXECUTION VERSION

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FIRST AMENDED AND RESTATED

LIMITED LIABILITY COMPANY AGREEMENT

HOLLY LOGISTIC SERVICES, L.L.C.

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TABLE OF CONTENTS

ARTICLE I
DEFINITIONS

Section 1.1 Definitions............................................................... 1
Section 1.2 Construction.............................................................. 5

ARTICLE II
ORGANIZATION

Section 2.1 Formation................................................................. 5
Section 2.2 Name...................................................................... 5
Section 2.3 Registered Office; Registered Agent; Principal Office; Other Offices...... 6
Section 2.4 Purpose and Business...................................................... 6
Section 2.5 Powers.................................................................... 6
Section 2.6 Term...................................................................... 7
Section 2.7 Title to Company Assets................................................... 7

ARTICLE III
RIGHTS OF MEMBERS

Section 3.1 Voting.................................................................... 7
Section 3.2 Distribution.............................................................. 7

ARTICLE IV
CAPITAL CONTRIBUTIONS; PRE EMPTIVE RIGHTS;
NATURE OF MEMBERSHIP INTEREST

Section 4.1 Initial Capital Contributions............................................. 7
Section 4.2 Additional Capital Contributions.......................................... 7
Section 4.3 Limited Preemptive Rights................................................. 8
Section 4.4 Fully Paid and Non-Assessable Nature of Membership Interests.............. 8
Section 4.5 Capital Account........................................................... 8

ARTICLE V
MANAGEMENT AND OPERATION OF BUSINESS

Section 5.1 Establishment of The Board................................................ 8
Section 5.2 The Board; Delegation of Authority and Duties............................. 8
Section 5.3 Term of Office............................................................ 9
Section 5.4 Meetings of the Board and Committees...................................... 10
Section 5.5 Voting.................................................................... 11
Section 5.6 Responsibility and Authority of the Board................................. 11
Section 5.7 Devotion of Time.......................................................... 11
Section 5.8 Certificate of Formation.................................................. 11
Section 5.9 Benefit Plans............................................................. 12
Section 5.10 Indemnification........................................................... 12

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

Section 5.11 Liability of Indemnitees.................................................. 14
Section 5.12 Reliance by Third Parties................................................. 14

ARTICLE VI
OFFICERS

Section 6.1 Officers.................................................................. 15
Section 6.2 Compensation.............................................................. 17

ARTICLE VII
BOOKS, RECORDS, ACCOUNTING AND REPORTS

Section 7.1 Records and Accounting.................................................... 17
Section 7.2 Reports................................................................... 17
Section 7.3 Bank Accounts............................................................. 17

ARTICLE VIII
DISSOLUTION AND LIQUIDATION

Section 8.1 Dissolution............................................................... 18
Section 8.2 Effect of Dissolution..................................................... 18
Section 8.3 Application of Proceeds................................................... 18
Section 8.4 Capital Account Restoration............................................... 19

ARTICLE IX
GENERAL PROVISIONS

Section 9.1 Addresses and Notices..................................................... 19
Section 9.2 Creditors................................................................. 19
Section 9.3 Applicable Law............................................................ 19
Section 9.4 Invalidity of Provisions.................................................. 20

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

THIS FIRST AMENDED AND RESTATED LIMITED LIABILTY COMPANY AGREEMENT of
Holly Logistic Services, L.L.C. (the "Company"), dated as of the Closing Date is
entered into by Navajo Pipeline Co., L.P., a Delaware limited partnership
("Navajo"), as sole member of the Company (the "Sole Member").

RECITALS:

WHEREAS, Navajo entered into a limited liability company agreement dated
effective as of December 18, 2003 for the purpose of forming the Company as a
limited liability company under the Delaware Limited Liability Company Act and
filed a Certificate of Formation with the Secretary of State of the State of
Delaware effective as of such date.

WHEREAS, Navajo now desires to execute this amended and restated Limited
Liability Company Agreement in connection with the initial public offering of
Holly Energy Partners, L.P., and certain other matters.

NOW THEREFORE, in consideration of the covenants, conditions and
agreements contained herein, the parties hereto hereby enter into this
Agreement:

ARTICLE I
DEFINITIONS

Section 1.1 Definitions.

The following definitions shall be for all purposes, unless otherwise
clearly indicated to the contrary, applied to the terms used in this Agreement.

"Act" means the Delaware Limited Liability Company Act, 6 Del. C. Section
18-101, et seq., as amended, supplemented or restated from time to time, and any
successor to such statute.

"Affiliate" means, with respect to any Person, any other Person that
directly or indirectly through one or more intermediaries controls, is
controlled by or is under common control with, the Person in question. As used
herein, the term "control" means the possession, direct or indirect, of the
power to direct or cause the direction of the management and policies of a
Person, whether through ownership of voting securities, by contract or
otherwise.

"Agreement" means this First Amended and Restated Limited Liability
Company Agreement of Holly Logistic Services, L.L.C., as it may be amended,
supplemented or restated

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

from time to time. The Agreement shall constitute a "limited liability company
agreement" as such term is defined in the Act.

"Associate" means, when used to indicate a relationship with any Person,
(a) any corporation or organization of which such Person is a director, officer
or partner or is, directly or indirectly, the owner of 20% or more of any class
of voting stock or other voting interest; (b) any trust or other estate in which
such Person has at least a 20% beneficial interest or as to which such Person
serves as trustee or in a similar fiduciary capacity; and (c) any relative or
spouse of such Person, or any relative of such spouse, who has the same
principal residence as such Person.

"Board" shall have the meaning assigned to such term in Section 5.1.

"Business Day" means Monday through Friday of each week, except that a
legal holiday recognized as such by the government of the United States of
America or the state of Texas shall not be regarded as a Business Day.

"Capital Contribution" means any cash, cash equivalents or the value of
Contributed Property contributed to the Company pursuant to this Agreement.

"Certificate of Formation" means the Certificate of Formation of the
Company filed with the Secretary of State of the State of Delaware as referenced
in Section 2.1, as such Certificate of Formation may be amended, supplemented or
restated from time to time.

"Closing Date" means the first date on which Common Units are sold by the
MLP to the Underwriters pursuant to the provisions of the Underwriting
Agreement.

"Code" means the Internal Revenue Code of 1986, as amended and in effect
from time to time. Any reference herein to a specific section or sections of the
Code shall be deemed to include a reference to any corresponding provision of
successor law.

"Commission" means the United States Securities and Exchange Commission.

"Common Unit" has the meaning assigned to such term in the MLP Agreement.

"Company" means Holly Logistic Services, L.L.C., a Delaware limited
liability company, and any successors thereto.

"Company Group" means the Company and any Subsidiary of the Company,
treated as a single consolidated entity.

"Contributed Property" means each property or other asset, in such form as
may be permitted by the Act, but excluding cash, contributed to the Company.

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

"Contribution Agreement" means that certain Contribution, Conveyance and
Assumption Agreement, dated as of the Closing Date, among the Company, Holly,
the MLP General Partner, the MLP, OLP GP, the OLP and certain other parties,
together with the additional conveyance documents and instruments contemplated
or referenced thereunder.

"Credit Agreement" means the Credit Agreement, dated July 7, 2004, among
the OLP, as borrower, and a syndicate of financial institutions led by Union
Bank of California as Administrative Agent and Sole Lead Arranger, Bank of
America, National Association, as Syndication Agent and Guaranty Bank, as
Documentation Agent.

"Directors" has the meaning assigned to such term in Section 5.1.

"Holly" means Holly Corporation, a Delaware corporation.

"Group Member" means a member of the Company Group.

"Indemnitee" means (a) the Sole Member; (b) any Person who is or was a
member, partner, director, officer, employee, agent or trustee of the Company,
any Group Member, the MLP, the General Partner or any of their respective
Affiliates; and (c) any Person who is or was serving at the request of the Sole
Member as a member, partner, director, officer, employee, partner, agent,
fiduciary or trustee of another Person, in each case, acting in such capacity,
provided, that a Person shall not be an Indemnitee by reason of providing, on a
fee-for-services basis, trustee, fiduciary or custodial services.

"Independent Director" has the meaning assigned to such term in Section
5.2.

"Initial Public Offering" means the initial offering and sale of Common
Units to the public, as described in the Registration Statement.

"Membership Interest" means all of the Sole Member's rights and interest
in the Company in the Sole Member's capacity as the Sole Member, all as provided
in the Certificate, this Agreement and the Act, including, without limitation,
the Sole Member's interest in the capital, income, gain, deductions, losses and
credits of the Company.

"MLP" means Holly Energy Partners, L.P.

"MLP Agreement" means the First Amended and Restated Agreement of Limited
Partnership of Holly Energy Partners, L.P., as it may be amended, supplemented
or restated from time to time.

"MLP General Partner" means HEP Logistics Holdings, L.P., a Delaware
limited partnership and the general partner of the MLP.

"NYSE" has the meaning assigned to such term in Section 5.2.

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

"Omnibus Agreement" means the Omnibus Agreement, dated as of the Closing
Date, among the Company, the MLP General Partner, Holly, Navajo, Navajo Refining
Company, L.P., the MLP, OLP GP and the OLP.

"Opinion of Counsel" means a written opinion of counsel (which may be
regular counsel to the Company or the MLP or any of their respective Affiliates)
acceptable to the Sole Member.

"Person" means an individual or a corporation, limited liability company,
partnership, joint venture, trust, unincorporated organization, association,
government agency or political subdivision thereof or other entity.

"Quarter" means, unless the context requires otherwise, a fiscal quarter
of the Company.

"Registration Statement" means, collectively, the Registration Statement
on Form S-1 (Registration No. 333-113588) as it has been or as it may be amended
or supplemented from time to time, filed by the MLP with the Commission under
the Securities Act to register the offering and sale of the Common Units in the
Initial Offering and the related Registration Statement on Form S-1
(Registration No.: 333-117217) filed by the MLP with the Commission pursuant to
Rule 462(b) under the Securities Act.

"Restricted Business" has the meaning assigned to such term in the Omnibus
Agreement.

"Securities Act" means the Securities Act of 1933, as amended,
supplemented or restated from time to time and any successor to such statute.

"Sole Member" means Navajo Pipeline Co., L.P. and its successors and
permitted assigns as sole member of the Company.

"Subsidiary" means, with respect to any Person, (a) a corporation of which
more than 50% of the voting power of shares entitled (without regard to the
occurrence of any contingency) to vote in the election of directors or other
governing body of such corporation is owned, directly or indirectly, at the date
of determination, by such Person, by one or more Subsidiaries of such Person or
a combination thereof; (b) a partnership (whether general or limited) in which
such Person or a Subsidiary of such Person is, at the date of determination, a
general or limited partner of such partnership, but only if more than 50% of the
partnership interests of such partnership (considering all of the partnership
interests of the partnership as a single class) is owned, directly or
indirectly, at the date of determination, by such Person, by one or more
Subsidiaries of such Person, or a combination thereof; or (c) any other Person
(other than a corporation or a partnership) in which such Person, one or more
Subsidiaries of such Person, or a combination thereof, directly or indirectly,
at the date of determination, has (i) at least a majority ownership interest or
(ii) the power to elect or direct the election of a majority of the directors or
other governing body of such Person.

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

"Underwriter" means each Person named as an underwriter in the
Underwriting Agreement who purchases Common Units pursuant thereto.

"Underwriting Agreement" means the Underwriting Agreement, dated as of the
July 7, 2004, among the Company, Navajo, the MLP General Partner, the MLP, OLP
GP, the OLP, Holly and the Underwriters, providing for the purchase of Common
Units by such Underwriters.

"Unit" has the meaning assigned to such term in the MLP Agreement.

"U.S. GAAP" means United States Generally Accepted Accounting Principles
consistently applied.

"Working Capital Borrowings" has the meaning assigned to such term in the
MLP Agreement.

Section 1.2 Construction.

(a) Unless the context requires otherwise: (i) capitalized terms used
herein but not otherwise defined shall have the meanings assigned to such terms
in the MLP Agreement; (ii) any pronoun used in this Agreement shall include the
corresponding masculine, feminine or neuter forms, and the singular form of
nouns, pronouns and verbs shall include the plural and vice versa; (iii)
references to Articles and Sections refer to Articles and Sections of this
Agreement; and (iv) the term "include" or "includes" means includes, without
limitation, and "including" means including, without limitation.

(b) A reference to any Person includes such Person's successors and
permitted assigns.

ARTICLE II
ORGANIZATION

Section 2.1 Formation.

On December 18, 2003, Navajo formed the Company as a limited liability
company pursuant to the provisions of the Act by virtue of the filing of the
Certificate of Formation with the Secretary of State of the State of Delaware.

Section 2.2 Name.

The name of the Company shall be "Holly Logistic Services, L.L.C.". The
Company's business may be conducted under any other name or names deemed
necessary or appropriate by the Board in its sole discretion, including, if
consented to by the Board, the name of the MLP. The words "Limited Liability
Company," "L.L.C." or "LLC" or similar words or letters shall be included in the
Company's name where necessary for the purpose of complying with the laws of

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

any jurisdiction that so requires. The Board in its discretion may change the
name of the Company at any time and from time to time and shall notify the Sole
Member of such change in the next regular communication to the Sole Member.

Section 2.3 Registered Office; Registered Agent; Principal Office; Other
Offices.

Unless and until changed by the Board, the registered office of the
Company in the State of Delaware shall be located at 1209 Orange Street, New
Castle County, Wilmington, Delaware 19801, and the registered agent for service
of process on the Company in the State of Delaware at such registered office
shall be The Corporation Trust Company. The principal office of the Company
shall be located at 100 Crescent Court, Suite 1600, Dallas, Texas 75201, or such
other place as the Board may from time to time designate. The Company may
maintain offices at such other place or places within or outside the State of
Delaware as the Board deems necessary or appropriate.

Section 2.4 Purpose and Business.

The purpose and nature of the business to be conducted by the Company
shall be to (a) serve as general partner of the MLP General Partner and, in
connection therewith, to exercise all rights and conferred upon the Company as
the general partner of the MLP General Partner pursuant to the First Amended and
Restated Agreement of Limited Partnership of the MLP General Partner, dated the
Closing Date, or otherwise, (b) engage directly in, or enter into or form any
corporation, partnership, joint venture, limited liability company or other
arrangement to engage indirectly in, any business activity that the Company is
permitted to engage in, or any type of business or activity engaged in by the
Company prior to the Closing Date and, in connection therewith, to exercise all
of the rights and powers conferred upon the Company pursuant to the agreements
relating to such business activity; (c) engage directly in, or enter into or
form any corporation, partnership, joint venture, limited liability company or
other arrangement to engage indirectly in, any business activity that is
approved by the Board and that lawfully may be conducted by a limited liability
company organized pursuant to the Act and, in connection therewith, to exercise
all of the rights and powers conferred upon the Company pursuant to the
agreements relating to such business activity; and (d) do anything necessary or
appropriate to the foregoing, including the making of capital contributions or
loans to a Group Member, the MLP or any Subsidiary of the MLP.

Section 2.5 Powers.

The Company shall be empowered to do any and all acts and things
necessary, appropriate, proper, advisable, incidental to or convenient for the
furtherance and accomplishment of the purposes and business described in Section
2.4 and for the protection and benefit of the Company.

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

Section 2.6 Term.

The term of the Company commenced upon the filing of the Certificate of
Formation in accordance with the Act and shall continue in existence in
perpetuity or until the earlier dissolution of the Company in accordance with
the provisions of Article VIII. The existence of the Company as a separate legal
entity shall continue until the cancellation of the Certificate of Formation as
provided in the Act.

Section 2.7 Title to Company Assets.

Title to Company assets, whether real, personal or mixed and whether
tangible or intangible, shall be deemed to be owned by the Company as an entity,
and the Sole Member shall not have any ownership interest in such Company assets
or any portion thereof.

ARTICLE III
RIGHTS OF MEMBERS

Section 3.1 Voting.

Unless otherwise granted to the Board this Agreement, the Sole Member
shall possess the entire voting interest in all matters relating to the Company,
including, without limitation, matters relating to the amendment of this
Agreement, any merger, consolidation or conversion of the Company, sale of all
or substantially all of the assets of the Company and the termination,
dissolution and liquidation of the Company.

Section 3.2 Distribution.

Distributions by the Company of cash or other property shall be made to
the Sole Member at such time as the Board deems appropriate.

ARTICLE IV
CAPITAL CONTRIBUTIONS; PRE EMPTIVE RIGHTS;
NATURE OF MEMBERSHIP INTEREST

Section 4.1 Initial Capital Contributions.

On December 18, 2003, in connection with the formation of the Company, the
Sole Member made a contribution to the capital of the Company in the amount of
$1,000 in exchange for all of the Membership Interests.

Section 4.2 Additional Capital Contributions.

The Sole Member shall not be obligated to make additional Capital
Contributions to the Company.

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

Section 4.3 Limited Preemptive Rights.

No Person shall have preemptive, preferential or other similar rights with
respect to (a) additional Capital Contributions; (b) issuance or sale of any
class or series of Membership Interests, whether unissued, held in the treasury
or hereafter created; (c) issuance of any obligations, evidences of indebtedness
or other securities of the Company convertible into or exchangeable for, or
carrying or accompanied by any rights to receive, purchase or subscribe to, any
such Membership Interests; (d) issuance of any right of subscription to or right
to receive, or any warrant or option for the purchase of, any such Membership
Interests; or (e) issuance or sale of any other securities that may be issued or
sold by the Company.

Section 4.4 Fully Paid and Non-Assessable Nature of Membership Interests.

All Membership Interests issued pursuant to, and in accordance with, the
requirements of this Article IV shall be fully paid and non-assessable
Membership Interests, except as such non-assessability may be affected by
Section 18-607 of the Act.

Section 4.5 Capital Account.

A "Capital Account" shall be maintained for the Sole Member in accordance
with the Code.

ARTICLE V
MANAGEMENT AND OPERATION OF BUSINESS

Section 5.1 Establishment of The Board.

The number of directors (the "Directors") constituting the Board shall be
seven, unless otherwise fixed from time to time pursuant to a resolution adopted
by the Sole Member. The Directors shall be elected or approved by the Sole
Member and shall serve as Directors of the Company until their death or removal
from office or until their successors are elected and qualified.

As at the date of this Agreement, the Directors of the Company are Matthew
P. Clifton and Lamar Norsworthy. The Sole Member intends to appoint Charles M.
Darling, IV, Jerry W. Pinkerton and William P. Stengel as Directors following
the Closing Date. In addition, the Sole Member intends to appoint two additional
Directors within 1 year of the date of this Agreement.

Section 5.2 The Board; Delegation of Authority and Duties.

(a) Members and Board. The business and affairs of the Company shall be
managed by the Board, which shall possess all rights and powers which are
possessed by "managers" under the Act and otherwise by applicable law, pursuant
to Section 18-402 of the Act, subject to the provisions of this Agreement.
Except as otherwise expressly provided for herein, the Sole

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

Member hereby consents to the exercise by the Board of all such powers and
rights conferred on it by the Act or otherwise by applicable law with respect to
the management and control of the Company. To the fullest extent permitted by
applicable law, each Director shall have such rights and duties as are
applicable to directors of a corporation organized under the General Corporation
Law of the State of Delaware.

(b) Delegation by the Board. The Board shall have the power and
authority to delegate to one or more other Persons the Board's rights and powers
to manage and control the business and affairs of the Company, including
delegating such rights and powers of the Board to agents and employees of the
Company (including Officers). The Board may authorize any Person (including,
without limitation, the Sole Member, or any Director or Officer) to enter into
any document on behalf of the Company and perform the obligations of the Company
thereunder. Notwithstanding the foregoing, the Board shall not have the power
and authority to delegate any rights or powers customarily requiring the
approval of the directors of a corporation and no Officer or other Person shall
be authorized or empowered to act on behalf of the Company in any way beyond the
customary rights and powers of an officer of a corporation.

(i) The Board may establish committees of the Board and may
delegate certain of its responsibilities to such committees.

(ii) The Board shall have an audit committee comprised of three
Directors, all of whom shall be Independent Directors. Such audit
committee shall establish a written audit committee charter in accordance
with the rules of the New York Stock Exchange, Inc. (the "NYSE"), as
amended from time to time. "Independent Director" shall mean Directors
meeting the independence and experience requirements as set forth most
recently by the NYSE. The initial members of the Audit Committee will be
Messrs. Darling, Pinkerton and Stengel.

(iii) The Board shall have a compensation committee (the
"Compensation Committee") which shall be charged with setting compensation
for officers of the Company, as well as administering any Incentive Plans
put in place by the Company. The initial members of the Compensation
Committee shall be Messrs. Darling, Pinkerton and Stengel.

Section 5.3 Term of Office.

Once designated pursuant to Section 5.1, a Director shall continue in
office until the removal of such Director in accordance with the provisions of
this Agreement or until the earlier death or resignation of such Director. Any
Director may resign at any time by giving written notice of such Director's
resignation to the Board. Any such resignation shall take effect at the time the
Board receives such notice or at any later effective time specified in such
notice. Unless

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

otherwise specified in such notice, the acceptance by the Board of such
Director's resignation shall not be necessary to make such resignation
effective. Notwithstanding anything herein or under applicable law to the
contrary, any Director may be removed at any time with or without cause by the
Sole Member.

Section 5.4 Meetings of the Board and Committees.

(a) Meetings. The Board (or any committee of the Board) shall meet at
such time and at such place as the Chairman of the Board (or the chairman of
such committee) may designate. Written notice of all regular meetings of the
Board (or any committee of the Board) must be given to all Directors (or all
members of such committee) at least ten days prior to the regular meeting of the
Board (or such committee). Special meetings of the Board (or any committee of
the Board) shall be held at the request of a majority of the Directors (or a
majority of the members of such committee) upon at least two days (if the
meeting is to be held in person) or twenty-four hours (if the meeting is to be
held telephonically) oral or written notice to the Directors (or the members of
such committee) or upon such shorter notice as may be approved by the Directors
(or the members of such committee). All notices and other communications to be
given to Directors (or members of a committee) shall be sufficiently given for
all purposes hereunder if in writing and delivered by hand, courier or overnight
delivery service or three days after being mailed by certified or registered
mail, return receipt requested, with appropriate postage prepaid, or when
received in the form of a telegram or facsimile, and shall be directed to the
address or facsimile number as such Director (or member) shall designate by
notice to the Company. Neither the business to be transacted at, nor the purpose
of, any regular or special meeting of the Board (or committee) need be specified
in the notice of such meeting. Any Director (or member of such committee) may
waive the requirement of such notice as to such Director (or such member).

(b) Conduct of Meetings. Any meeting of the Board (or any committee of
the Board) may be held in person or by conference telephone or similar
communications equipment by means of which all persons participating in the
meeting can hear each other, and such participation in a meeting shall
constitute presence in person at such meeting.

(c) Quorum. A majority of all Directors (or members of a committee of
the Board), present in person or participating in accordance with Section
5.4(b), shall constitute a quorum for the transaction of business, but if at any
meeting of the Board (or committee) there shall be less than a quorum present, a
majority of the Directors (or members) present may adjourn the meeting without
further notice. The Directors (or members of a committee of the Board) present
at a duly organized meeting may continue to transact business until adjournment,
notwithstanding the withdrawal of enough Directors (or members) to leave less
than a quorum; provided, however, that only the acts of the Directors (or
members) meeting the requirements of Section 5.5 shall be deemed to be acts of
the Board (or such committee).

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

(d) Procedures. To the extent not inconsistent with this Agreement or
the Act, the procedures and rights governing the Board and its committees shall
be as provided to the board of directors and its committees of a corporation
under the General Corporation Law of the State of Delaware.

(e) Chairman of the Board. The chairman of the Board shall preside at
all meetings of the Board. The Directors also may elect a vice-chairman to act
in the place of the chairman upon his absence or inability to act.

Section 5.5 Voting.

Except as otherwise provided in this Agreement, the effectiveness of any
vote, consent or other action of the Board (or any committee of the Board) in
respect of any matter shall require either (i) the presence of a quorum and the
affirmative vote of greater than a majority of the Directors (or members of such
committee) present or (ii) the unanimous written consent (in lieu of meeting) of
the Directors (or members of such committee) who have been designated and who
are then in office. Any Director may vote in person or by proxy (pursuant to a
power of attorney) on any matter that is to be voted on by the Board at a
meeting thereof.

Section 5.6 Responsibility and Authority of the Board.

Except as otherwise specifically provided in this Agreement, the authority
and functions of the Board, on the one hand, and the Officers, on the other
hand, shall be identical to the authority and functions of the board of
directors and officers, respectively, of a corporation organized under the
General Corporation Law of the State of Delaware. The Officers shall be vested
with such powers and duties as are set forth in Section 6.1 hereof and as are
specified by the Board from time to time. Accordingly, except as otherwise
specifically provided in this Agreement, the business and affairs of the Company
shall be managed under the direction of the Board, and the day-to-day activities
of the Company shall be conducted on the Company's behalf by the Officers who
shall be agents of the Company.

Section 5.7 Devotion of Time.

The Directors shall not be obligated and shall not be expected to devote
all of their time or business efforts to the affairs of the Company (except in
their capacity as employees of the Company).

Section 5.8 Certificate of Formation.

Navajo caused the Certificate of Formation to be filed with the Secretary
of State of the State of Delaware as required by the Act and certain other
certificates or documents it determined in its sole discretion to be necessary
or appropriate for the qualification and operation of the Company in certain
other states. The Sole Member shall use all reasonable efforts to cause to be
filed such additional certificates or documents as may be determined by the Sole

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LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

Member to be necessary or appropriate for the formation, continuation,
qualification and operation of a limited liability company in the State of
Delaware or any other state in which the Company may elect to do business or own
property. To the extent that such action is determined by the Sole Member to be
necessary or appropriate, the Sole Member shall file amendments to and
restatements of the Certificate of Formation and do all things to maintain the
Company as a limited liability company under the laws of the State of Delaware
or of any other state in which the Company may elect to do business or own
property.

Section 5.9 Benefit Plans.

The Board may propose and adopt on behalf of the Company employee benefit
plans, employee programs and employee practices, or cause the Company to issue
Company Securities, in connection with or pursuant to any employee benefit plan,
employee program or employee practice maintained or sponsored by any Group
Member or any Affiliate thereof, in each case for the benefit of employees of
the Company, any Group Member or any Affiliate thereof, or any of them, in
respect of services performed, directly or indirectly, for the benefit of the
Company Group.

Section 5.10 Indemnification.

(a) To the fullest extent permitted by law but subject to the
limitations expressly provided in this Agreement, all Indemnitees shall be
indemnified and held harmless by the Company from and against any and all
losses, damages or liabilities, joint or several, expenses (including legal fees
and expenses), judgments, fines, penalties, interest, settlements or other
amounts arising from any and all claims, demands, actions, suits or proceedings,
whether civil, criminal, administrative or investigative, in which any
Indemnitee may be involved, or is threatened to be involved, as a party or
otherwise, by reason of its status as an Indemnitee; provided, that the
Indemnitee shall not be indemnified and held harmless if there has been a final
and non-appealable judgment entered by a court of competent jurisdiction
determining that, in respect of the matter for which the Indemnitee is seeking
indemnification pursuant to this Section 5.10, the Indemnitee acted in bad faith
or engaged in fraud, willful misconduct or gross negligence or, in the case of a
criminal matter, acted with knowledge that the Indemnitee's conduct was
unlawful. Any indemnification pursuant to this Section 5.10 shall be made only
out of the assets of the Company, it being agreed that the Sole Member shall not
be personally liable for such indemnification and shall have no obligation to
contribute or loan any monies or property to the Company to enable it to
effectuate such indemnification.

(b) To the fullest extent permitted by law, expenses (including legal
fees and expenses) incurred by an Indemnitee who is indemnified pursuant to
Section 5.10(a) in defending any claim, demand, action, suit or proceeding
shall, from time to time, be advanced by the Company prior to a determination
that the Indemnitee is not entitled to be indemnified upon receipt by the
Company of any undertaking by or on behalf of the Indemnitee to repay such

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LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

amount if it shall be determined that the Indemnitee is not entitled to be
indemnified as authorized in this Section 5.10.

(c) The indemnification provided by this Section 5.10 shall be in
addition to any other rights to which an Indemnitee may be entitled under any
agreement, pursuant to any decision of the Sole Member, as a matter of law or
otherwise, both as to actions in the Indemnitee's capacity as an Indemnitee and
as to actions in any other capacity (including any capacity under the
Underwriting Agreement), and shall continue as to an Indemnitee who has ceased
to serve in such capacity and shall inure to the benefit of the heirs,
successors, assigns and administrators of the Indemnitee.

(d) The Company may purchase and maintain (or reimburse the Sole Member
or its Affiliates for the cost of) insurance, on behalf of the Directors, the
Officers, the Sole Member, its Affiliates and such other Persons as the Sole
Member shall determine, against any liability that may be asserted against or
expense that may be incurred by such Person in connection with the Company's
activities or such Person's activities on behalf of the Company, regardless of
whether the Company would have the power to indemnify such Person against such
liability under the provisions of this Agreement.

(e) For purposes of this Section 5.10, the Company shall be deemed to
have requested an Indemnitee to serve as fiduciary of an employee benefit plan
whenever the performance by it of its duties to the Company also imposes duties
on, or otherwise involves services by, it to the plan or participants or
beneficiaries of the plan; excise taxes assessed on an Indemnitee with respect
to an employee benefit plan pursuant to applicable law shall constitute "fines"
within the meaning of Section 5.10(a); and action taken or omitted by it with
respect to any employee benefit plan in the performance of its duties for a
purpose reasonably believed by it to be in the interest of the participants and
beneficiaries of the plan shall be deemed to be for a purpose which is in the
best interests of the Company.

(f) In no event may an Indemnitee subject the Sole Member to personal
liability by reason of the indemnification provisions set forth in this
Agreement.

(g) An Indemnitee shall not be denied indemnification in whole or in
part under this Section 5.10 because the Indemnitee had an interest in the
transaction with respect to which the indemnification applies if the transaction
was otherwise permitted by the terms of this Agreement.

(h) The provisions of this Section 5.10 are for the benefit of the
Indemnitees, their heirs, successors, assigns and administrators and shall not
be deemed to create any rights for the benefit of any other Persons.

(i) No amendment, modification or repeal of this Section 5.10 or any
provision hereof shall in any manner terminate, reduce or impair the right of
any past, present or future

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LIMITED LIABILITY COMPANY AGREEMENT
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HOLLY LOGISTIC SERVICES, L.L.C.

Indemnitee to be indemnified by the Company, nor the obligations of the Company
to indemnify any such Indemnitee under and in accordance with the provisions of
this Section 5.10 as in effect immediately prior to such amendment, modification
or repeal with respect to claims arising from or relating to matters occurring,
in whole or in part, prior to such amendment, modification or repeal, regardless
of when such claims may arise or be asserted.

Section 5.11 Liability of Indemnitees.

(a) Notwithstanding anything to the contrary set forth in this Agreement
or the MLP Agreement, no Indemnitee shall be liable for monetary damages to the
Company, the Sole Member or any other Persons who have acquired interests in the
MLP, for losses sustained or liabilities incurred as a result of any act or
omission if such Indemnitee acted in good faith.

(b) Any amendment, modification or repeal of this Section 5.11 or any
provision hereof shall be prospective only and shall not in any way affect the
limitations on the liability of the Indemnitees under this Section 5.11 as in
effect immediately prior to such amendment, modification or repeal with respect
to claims arising from or relating to matters occurring, in whole or in part,
prior to such amendment, modification or repeal, regardless of when such claims
may arise or be asserted.

Section 5.12 Reliance by Third Parties.

Notwithstanding anything to the contrary in this Agreement, any Person
dealing with the Company shall be entitled to assume that any Officer authorized
by the Board to act for and on behalf of and in the name of the Company has full
power and authority to encumber, sell or otherwise use in any manner any and all
assets of the Company and to enter into any authorized contracts on behalf of
the Company, and such Person shall be entitled to deal with any such Officer as
if it were the Company's sole party in interest, both legally and beneficially.
The Sole Member hereby waives any and all defenses or other remedies that may be
available against such Person to contest, negate or disaffirm any action of any
such Officer in connection with any such dealing. In no event shall any Person
dealing with any such Officer or its representatives be obligated to ascertain
that the terms of the Agreement have been complied with or to inquire into the
necessity or expedience of any act or action of any such Officer or its
representatives. Each and every certificate, document or other instrument
executed on behalf of the Company by any Officer authorized by the Board shall
be conclusive evidence in favor of any and every Person relying thereon or
claiming thereunder that (a) at the time of the execution and delivery of such
certificate, document or instrument, this Agreement was in full force and
effect, (b) the Person executing and delivering such certificate, document or
instrument was duly authorized and empowered to do so for and on behalf of and
in the name of the Company and (c) such certificate, document or instrument was
duly executed and delivered in accordance with the terms and provisions of this
Agreement and is binding upon the Company.

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LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

ARTICLE VI
OFFICERS

Section 6.1 Officers.

(a) Generally. The Board shall appoint agents of the Company, referred
to as "Officers" of the Company as described in this Section 6.1, who shall be
responsible for the day-to-day business affairs of the Company, subject to the
overall direction and control of the Board. Unless provided otherwise by Board,
the Officers shall have the titles, power, authority and duties described below
in this Section 6.1.

(b) Titles and Number. The Officers shall be the Chairman, the Chief
Executive Officer, any and all Vice Presidents, the Secretary and any and all
Assistant Secretaries and any Treasurer and any and all Assistant Treasurers and
any other Officers appointed pursuant to this Section 6.1. There shall be
appointed from time to time, in accordance with this Section 6.1, such Vice
Presidents, Secretaries, Assistant Secretaries, Treasurers and Assistant
Treasurers as the Board may desire. Any person may hold two or more offices.

(i) Chairman. The Board shall elect an individual to serve as
Chairman. The Chairman shall preside at all meetings of the Board. The
Board may also elect a Vice Chairman to act in place of the Chairman in
his absence. The Chairman of the Board may also be the Chief Executive
Officer.

(ii) Chief Executive Officer. The Board shall elect an individual
to serve as Chief Executive Officer. In general, the Chief Executive
Officer, subject to the direction and supervision of the Board and the
Chairman, shall be the chief executive officer of the Company and shall
have general and active control of the general management and affairs and
business and general supervision of the Company and officers, agents and
employees, and shall perform all duties incident to the office of Chief
Executive Officer of the Company and such other duties as may be
prescribed from time to time by the Board or the Chairman. The Chief
Executive Officer shall have the nonexclusive authority to sign on behalf
of the Company any deeds, mortgages, leases, bonds, notes, certificates,
contracts or other instruments, except in cases where the execution
thereof shall be expressly delegated by the Board, the Chairman, or by
this Agreement to some other officer or agent of the Company or shall be
required by law to be otherwise executed. In the absence of the Chairman,
or the Vice Chairman, if there is one, or in the event of the Chairman's
inability or refusal to act, the Chief Executive Officer shall perform the
duties of the Chairman, and the Chief Executive Officer, when so acting,
shall have all of the powers of the Chairman.

(iii) Vice Presidents. The Board, in its discretion, may elect one
or more Vice Presidents. In the absence of the Chief Executive Officer or
in the event of the Chief Executive Officer's inability or refusal to act,
the Vice President (or in the event there be

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LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

more than one vice president, the vice presidents in the order designated,
or in the absence of any designation, then in the order of their election)
shall perform the duties of the Chief Executive Officer, and the Vice
President, when so acting, shall have all of the powers and be subject to
all the restrictions upon the Chief Executive Officer. Each Vice President
shall perform such other duties as from time to time may be assigned by
the President or the Board.

(iv) Secretary and Assistant Secretaries. The Board, in its
discretion, may elect a Secretary and one or more Assistant Secretaries.
The Secretary shall record or cause to be recorded in books provided for
that purpose the minutes of the meetings or actions of the Board and of
the Sole Member, shall see that all notices are duly given in accordance
with the provisions of this Agreement and as required by law, shall be
custodian of all records (other than financial), shall see that the books,
reports, statements, certificates and all other documents and records
required by law are properly kept and filed, and, in general, shall
perform all duties incident to the office of Secretary and such other
duties as may, from time to time, be assigned to him by this Agreement,
the Board or the Chief Executive Officer. The Assistant Secretaries shall
exercise the powers of the Secretary during that Officer's absence or
inability or refusal to act.

(v) Treasurer and Assistant Treasurers. The Board, in its
discretion, may elect a Treasurer and one or more Assistant Treasurers.
The Treasurer shall keep or cause to be kept the books of account of the
Company and shall render statements of the financial affairs of the
Company in such form and as often as required by this Agreement, the Board
or the Chief Executive Officer. The Treasurer, subject to the order of the
Board, shall have the custody of all funds and securities of the Company.
The Treasurer shall perform all other duties commonly incident to his
office and shall perform such other duties and have such other powers as
this Agreement, the Board or the Chief Executive Officer, shall designate
from time to time. The Assistant Treasurers shall exercise the power of
the Treasurer during that Officer's absence or inability or refusal to
act. Each of the Assistant Treasurers shall possess the same power as the
Treasurer to sign all certificates, contracts, obligations and other
instruments of the Company. If no Treasurer or Assistant Treasurer is
appointed and serving or in the absence of the appointed Treasurer and
Assistant Treasurer, the Chief Executive Officer or such other Officer as
the Board shall select, shall have the powers and duties conferred upon
the Treasurer.

(c) Other Officers and Agents. The Board may appoint such other Officers
and agents as may from time to time appear to be necessary or advisable in the
conduct of the affairs of the Company, who shall hold their offices for such
terms and shall exercise such powers and perform such duties as shall be
determined from time to time by the Board.

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HOLLY LOGISTIC SERVICES, L.L.C.

(d) Appointment and Term of Office. The Officers shall be appointed by
the Board at such time and for such terms as the Board shall determine. Any
Officer may be removed, with or without cause, only by the Board. Vacancies in
any office may be filled only by the Board.

(e) Powers of Attorney. The Board may grant powers of attorney or other
authority as appropriate to establish and evidence the authority of the Officers
and other Persons.

(f) Officers' Delegation of Authority. Unless otherwise provided by
resolution of the Board, no Officer shall have the power or authority to
delegate to any Person such Officer's rights and powers as an Officer to manage
the business and affairs of the Company.

Section 6.2 Compensation.

The Officers shall receive such compensation for their services as may be
designated by the Compensation Committee.

ARTICLE VII
BOOKS, RECORDS, ACCOUNTING AND REPORTS

Section 7.1 Records and Accounting.

The Board shall keep or cause to be kept at the principal office of the
Company appropriate books and records with respect to the Company's business.
The books of account of the Company shall be (i) maintained on the basis of a
fiscal year that is the calendar year and (ii) maintained on an accrual basis in
accordance with GAAP, consistently applied.

Section 7.2 Reports.

With respect to each calendar year, the Board shall prepare, or cause to
be prepared, and deliver, or cause to be delivered, to the Sole Member:

(a) Within 120 Days after the end of such calendar year, a profit and
loss statement and a statement of cash flows for such year and a balance sheet
as of the end of such year.

(b) Such federal, state and local income tax returns and such other
accounting, tax information and schedules as shall be necessary for the
preparation by the Sole Member on or before June 15 following the end of each
calendar year of its income tax return with respect to such year.

Section 7.3 Bank Accounts.

Funds of the Company shall be deposited in such banks or other
depositories as shall be designated from time to time by the Board. All
withdrawals from any such depository shall be

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

made only as authorized by the Board and shall be made only by check, wire
transfer, debit memorandum or other written instruction.

ARTICLE VIII
DISSOLUTION AND LIQUIDATION

Section 8.1 Dissolution.

(a) The Company shall be of perpetual duration; however, the Company
shall dissolve, and its affairs shall be wound up, upon:

(i) an election to dissolve the Company by the Sole Member;

(ii) the entry of a decree of judicial dissolution of the Company
pursuant to the provisions of the Act; or

(iii) a merger or consolidation under the Act where the Company is
not the surviving entity in such merger or consolidation.

(b) No other event shall cause a dissolution of the Company.

Section 8.2 Effect of Dissolution.

Except as otherwise provided in this Agreement, upon the dissolution of
the Company, the Sole Member shall take such actions as may be required pursuant
to the Act and shall proceed to wind up, liquidate and terminate the business
and affairs of the Company. In connection with such winding up, the Sole Member
shall have the authority to liquidate and reduce to cash (to the extent
necessary or appropriate) the assets of the Company as promptly as is consistent
with obtaining fair value therefor, to apply and distribute the proceeds of such
liquidation and any remaining assets in accordance with the provisions of
Section 8.3(c), and to do any and all acts and things authorized by, and in
accordance with, the Act and other applicable laws for the purpose of winding up
and liquidation.

Section 8.3 Application of Proceeds.

Upon dissolution and liquidation of the Company, the assets of the Company
shall be applied and distributed in the following order of priority:

(a) To the payment of debts and liabilities of the Company (including to
the Sole Member to the extent permitted by applicable law) and the expenses of
liquidation.

(b) Next, to the setting up of such reserves as the Person required or
authorized by law to wind up the Company's affairs may reasonably deem necessary
or appropriate for any disputed, contingent or unforeseen liabilities or
obligations of the Company, provided that any

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LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

such reserves shall be paid over by such Person to an escrow agent appointed by
the Board, to be held by such agent or its successor for such period as such
Person shall deem advisable for the purpose of applying such reserves to the
payment of such liabilities or obligations and, at the expiration of such
period, the balance of such reserves, if any, shall be distributed as
hereinafter provided.

Section 8.4 Capital Account Restoration.

The Sole Member shall not have any obligation to restore any negative
balance in its Capital Account upon liquidation of the Company.

ARTICLE IX
GENERAL PROVISIONS

Section 9.1 Addresses and Notices.

Any notice, demand, request, report or proxy materials required or
permitted to be given or made to the Sole Member under this Agreement shall be
in writing and shall be deemed given or made when delivered in person or when
sent by first class United States mail or by other means of written
communication to the Sole Member at the address described below. Any notice to
the Company shall be deemed given if received by the Chief Executive Officer at
the principal office of the Company designated pursuant to Section 2.3. The
Company may rely and shall be protected in relying on any notice or other
document from the Sole Member or other Person if believed by it to be genuine.

If to the Sole Member:

Navajo Pipeline Co., L.P.
100 Crescent Court, Suite 1600
Dallas, Texas 75201
Attn: President
Facsimile No.: (214) __________

Section 9.2 Creditors.

None of the provisions of this Agreement shall be for the benefit of, or
shall be enforceable by, any creditor of the Company.

Section 9.3 Applicable Law.

This Agreement shall be construed in accordance with and governed by the
laws of the State of Delaware, without regard to the principles of conflicts of
law.

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

Section 9.4 Invalidity of Provisions.

If any provision of this Agreement is or becomes invalid, illegal or
unenforceable in any respect, the validity, legality and enforceability of the
remaining provisions contained herein shall not be affected thereby.

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LIMITED LIABILITY COMPANY AGREEMENT
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HOLLY LOGISTIC SERVICES, L.L.C.

IN WITNESS WHEREOF, the undersigned has executed this Agreement as of the
date first written above.

NAVAJO PIPELINE CO., L.P.

By: NAVAJO PIPELINE GP, L.L.C.
its General Partner

By: /s/ Stephen J. McDonnell
------------------------------------------
Stephen J. McDonnell
Vice President and Chief Financial Officer

FIRST AMENDED AND RESTATED
LIMITED LIABILITY COMPANY AGREEMENT
OF
HOLLY LOGISTIC SERVICES, L.L.C.

SIGNATURE PAGE