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As filed with the Securities and Exchange Commission on January 19, 2016

Registration No. 333-            

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form S-4

REGISTRATION STATEMENT

UNDER

THE SECURITIES ACT OF 1933

WESTERN REFINING, INC.

(Exact name of registrant as specified in its charter)

123 West Mills Avenue, Suite 200

El Paso, Texas 79901

(915) 534-1400

(Address, including zip code, and telephone number, including area code, of registrant’s principal executive offices)

Lowry Barfield

Senior Vice President – Legal, General Counsel and Secretary

123 West Mills Avenue, Suite 200

El Paso, Texas 79901

(915) 534-1400

(Name, address, including zip code, and telephone number, including area code, of agent for service)

Approximate date of commencement of proposed sale of the securities to the public: As soon as practicable after this registration statement becomes effective and upon consummation of the merger described in the enclosed proxy statement/prospectus.

If the securities being registered on this Form are to be offered in connection with the formation of a holding company and there is compliance with General Instruction G, check the following box.  ¨

If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.  ¨

If this Form is a post-effective amendment filed pursuant to Rule 462(d) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.  ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

If applicable, place an X in the box to designate the appropriate rule provision relied upon in conducting this transaction:

Exchange Act Rule 13e-4(i) (Cross-Border Issuer Tender Offer)  ¨

Exchange Act Rule 14d-1(d) (Cross-Border Third-Party Tender Offer)  ¨

CALCULATION OF REGISTRATION FEE

The Registrant hereby amends this Registration Statement on such date or dates as may be necessary to delay its effective date until the Registrant shall file a further amendment which specifically states that this Registration Statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933 or until this Registration Statement shall become effective on such date as the Securities and Exchange Commission, acting pursuant to said Section 8(a), may determine.

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The information in this preliminary proxy statement/prospectus is not complete and may be changed. Western Refining, Inc. may not distribute or issue the securities being registered pursuant to this registration statement until the registration statement, as filed with the Securities and Exchange Commission (of which this preliminary proxy statement/prospectus is a part), is effective. This preliminary proxy statement/prospectus is not an offer to sell nor should it be considered a solicitation of an offer to buy the securities described herein in any state where the offer or sale is not permitted.

PRELIMINARY PROXY STATEMENT/PROSPECTUS—SUBJECT TO COMPLETION—

DATED JANUARY 19, 2016

MERGER PROPOSAL—YOUR VOTE IS VERY IMPORTANT

On December 21, 2015, Western Refining, Inc. (“WNR”), Western Acquisition Co, LLC (“MergerCo”), an indirect wholly-owned subsidiary of WNR, Northern Tier Energy LP (“NTI”) and Northern Tier Energy GP LLC (“NTI GP”), an indirect wholly-owned subsidiary of WNR and the general partner of NTI, entered into an agreement and plan of merger (as such agreement may be amended from time to time, the “Merger Agreement”). Pursuant to the Merger Agreement, MergerCo will merge with and into NTI (the “Merger”), with NTI surviving the Merger as an indirect wholly-owned subsidiary of WNR, and each common unit representing limited partner interests in NTI (“NTI Common Units”) issued and outstanding immediately prior to the effective time of the Merger and not owned by WNR or any of its subsidiaries will be converted into the right to receive $15.00 in cash without interest and 0.2986 of a share of WNR’s common stock, par value $0.01 per share (“WNR Common Stock”) (which we refer to as the “Mixed Election” or the “Standard Mix of Consideration”). Instead of receiving the Standard Mix of Consideration, each NTI common unitholder other than WNR and its subsidiaries will have an opportunity to make an election to receive $26.06 in cash without interest (which we refer to as a “Cash Election”) or to receive 0.7036 of a share of WNR Common Stock (which we refer to as a “Stock Election”), for each NTI Common Unit they own immediately prior to the Merger. The Cash Election and Stock Election, however, will be subject to proration to ensure that the total amount of cash paid and the total number of shares of WNR Common Stock issued in the Merger to NTI common unitholders as a whole are equal to the total amount of cash and number of shares of WNR Common Stock that would have been paid and delivered if all NTI common unitholders other than WNR and its subsidiaries received the Standard Mix of Consideration.

Pursuant to the terms of the Merger Agreement, with respect to the quarter in which the closing date of the Merger (the “Closing Date”) occurs, NTI will, to the extent it generates available cash in such quarter, make a prorated quarterly cash distribution to NTI common unitholders of record as of immediately prior to the effective time of the Merger of such available cash if the record date for the WNR quarterly cash dividend to be paid in that quarter occurs before the Closing Date. Accordingly, in the quarter that the Closing Date occurs, NTI common unitholders who receive WNR Common Stock in the Merger will receive (i) an NTI cash distribution in respect of the previous quarter, to the extent NTI generates available cash in such quarter; and (ii) either an NTI prorated cash distribution in respect of available cash generated by NTI in the quarter in which the Closing Date occurs or (assuming such unitholders continue to hold the shares of WNR Common Stock received in the Merger through the record date for such WNR dividend) the WNR quarterly cash dividend payable in the quarter in which the Closing Date occurs. The amount of any distribution will not have any effect on the merger consideration to be received by NTI common unitholders.

No fractional shares of WNR Common Stock will be issued in the Merger. NTI common unitholders will receive cash (without interest and rounded up to the nearest whole cent) in lieu of receiving any fractional shares of WNR Common Stock to which any NTI common unitholder would otherwise have been entitled. WNR stockholders will continue to own their existing shares of WNR Common Stock.

Based on the estimated number of shares of WNR Common Stock and the estimated number of NTI Common Units that will be outstanding immediately before the closing of the Merger (other than NTI Common Units owned by WNR or any of its subsidiaries), we estimate that, upon the closing, the number of shares of WNR Common Stock issued in exchange for NTI Common Units will represent approximately 15% of WNR Common Stock outstanding immediately after the Merger.

The Merger Agreement requires that, prior to the Closing Date, the Merger Agreement and the transactions contemplated thereby (the “Merger Transactions”) be approved by the affirmative vote of NTI common unitholders, as of the record date for the NTI special meeting, holding a majority of the outstanding NTI Common Units. NTI will hold a special meeting of its common unitholders in connection with the proposed Merger. At the special meeting of NTI common unitholders, NTI common unitholders will be asked to vote on

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the proposal to approve the Merger Agreement and the Merger Transactions, including the Merger (the “Merger Proposal”). The Merger Proposal will be approved by the requisite vote of the NTI common unitholders if the holders, as of the record date of the NTI special meeting, of a majority of the outstanding NTI Common Units vote in favor of the Merger Proposal at the NTI special meeting. Pursuant to the Merger Agreement, WNR has agreed to vote the NTI Common Units owned beneficially or of record by it or any of its subsidiaries in favor of the adoption and approval of the Merger Agreement and the Merger Transactions. As of the close of business on [            ], 2016, the record date for the NTI special meeting, WNR held 35,622,500 NTI Common Units, representing approximately 38.4% of the outstanding NTI Common Units.

At the special meeting of NTI common unitholders, NTI common unitholders will also be asked to vote on a proposal to approve, on an advisory, non-binding basis, the compensation payments that may be paid or become payable to NTI’s named executive officers in connection with the Merger (the “NTI Compensation Proposal”). Approval, on an advisory, non-binding basis, of the NTI Compensation Proposal requires the affirmative vote of a majority of the outstanding NTI Common Units present in person or represented by proxy and entitled to vote at the NTI special meeting.

The conflicts committee (the “NTI GP Conflicts Committee”) of the board of directors of NTI GP (the “NTI GP Board”), acting on behalf of NTI GP, in its capacity as the general partner of NTI, approved the Merger Agreement and the Merger Transactions and determined that the Merger Agreement and the Merger Transactions are fair and reasonable to the holders of NTI Common Units other than WNR and its affiliates (the “NTI Unaffiliated Unitholders”) and NTI, and are not adverse to the interests of the NTI Unaffiliated Unitholders or the interests of NTI. The NTI GP Conflicts Committee’s approval of the Merger Agreement and the Merger Transactions constitutes “Special Approval,” as such term is defined by the NTI partnership agreement. The NTI GP Conflicts Committee, acting on behalf of NTI GP, in its capacity as the general partner of NTI, has called an NTI special meeting and has directed that the Merger Agreement and the Merger Transactions be submitted to the NTI common unitholders at the NTI special meeting for approval. The NTI GP Conflicts Committee recommends that the NTI common unitholders vote in favor of the Merger Proposal and in favor of the NTI Compensation Proposal.

This proxy statement/prospectus provides you with detailed information about the Merger Agreement, the proposed Merger and related matters. We encourage you to read the entire document carefully. In particular, please read “Risk Factors” beginning on page 106 of this proxy statement/prospectus for a discussion of risks related to the Merger, ownership of WNR Common Stock and material U.S. federal income tax consequences of the Merger.

Shares of WNR Common Stock are listed on the New York Stock Exchange (“NYSE”) under the symbol “WNR,” and NTI Common Units are listed on the NYSE under the symbol “NTI.” The last reported sale price of shares of WNR Common Stock on the NYSE on                 , 2016 was $[●]. The last reported sale price of NTI Common Units on the NYSE on                 , 2016 was $[●].

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of the securities to be issued under this proxy statement/prospectus or has determined if this proxy statement/prospectus is truthful or complete. Any representation to the contrary is a criminal offense.

All information in this proxy statement/prospectus concerning WNR has been furnished by WNR. All information in this proxy statement/prospectus concerning NTI has been furnished by NTI.

This proxy statement/prospectus is dated                 , 2016, and is being first mailed to NTI common unitholders on or about                 , 2016.

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Tempe, Arizona

        , 2016

Notice of Special Meeting of Common Unitholders

To the Common Unitholders of Northern Tier Energy LP:

A special meeting of common unitholders of Northern Tier Energy LP (“NTI”) will be held on                 , 2016 at 9:00 a.m., Tempe, Arizona Time, in                 , located on the Floor of                 ,                 , for the following purposes:

NTI will transact no other business at the special meeting except such business as may properly be brought before the special meeting or any adjournments or postponements thereof. At this time, NTI knows of no other matters that will be presented for the consideration of its common unitholders at the special meeting.

The Merger Proposal will be approved by the requisite vote of the NTI common unitholders if the holders, as of the record date of the NTI special meeting, of a majority of the outstanding NTI common units (“NTI Common Units”) vote in favor of the Merger Proposal. Failure to vote, abstentions and broker non-votes (if any) will have the same effect as a vote against the Merger Proposal. Approval, on an advisory, non-binding basis, of the NTI Compensation Proposal requires the affirmative vote of a majority of the outstanding NTI common units present in person or represented by proxy and entitled to vote at the NTI special meeting. Abstentions will have the same effect as a vote against the NTI Compensation Proposal. Broker non-votes (if any) will have no effect on the NTI Compensation Proposal. Pursuant to the Merger Agreement, WNR has agreed to vote the NTI Common Units owned beneficially or of record by it or any of its subsidiaries in favor of the approval of the Merger Agreement and the Merger Transactions. As of the close of business on                 , 2016, the record date for the NTI special meeting, WNR held 35,622,500 NTI Common Units, representing approximately 38.4% of the outstanding NTI Common Units. Because the vote on the NTI Compensation Proposal is advisory in nature only, it will not be binding on NTI or WNR.

The conflicts committee (the “NTI GP Conflicts Committee”) of the board of directors of NTI GP (the “NTI GP Board”), acting on behalf of NTI GP, in its capacity as the general partner of NTI, approved the Merger Agreement and the Merger Transactions and determined that the Merger Agreement and the Merger Transactions are fair and reasonable to the holders of NTI Common Units other than WNR and its affiliates (the “NTI Unaffiliated Unitholders”) and NTI, and are not adverse to the interests of the NTI Unaffiliated Unitholders or the interests of NTI. The NTI GP Conflicts Committee’s approval of the Merger Agreement and the Merger Transactions constitutes “Special Approval,” as such term is defined by the NTI partnership agreement. The NTI GP Conflicts Committee, acting on behalf of NTI GP, in its capacity as the general partner of NTI, has called this special meeting and has directed that the Merger

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Agreement and the Merger Transactions be submitted to the NTI common unitholders at the NTI special meeting for approval. The NTI GP Conflicts Committee recommends that the NTI common unitholders vote in favor of the Merger Proposal and the NTI Compensation Proposal.

Only NTI common unitholders of record as of the close of business on                 , 2016, are entitled to notice of and to vote at the special meeting and any adjournments of the special meeting. A list of NTI common unitholders entitled to vote at the NTI special meeting will be available for inspection to the NTI common unitholders of record at NTI’s offices in Tempe, Arizona, for any purpose relevant to the special meeting during normal business hours for a period of ten days before the special meeting and at the special meeting.

YOUR VOTE IS IMPORTANT. WHETHER OR NOT YOU EXPECT TO ATTEND THE SPECIAL MEETING, PLEASE CAUSE YOUR UNITS TO BE VOTED IN ONE OF THE FOLLOWING WAYS:

The enclosed proxy statement/prospectus provides a detailed description of the Merger Transactions and the Merger Agreement as well as a description of the WNR Common Stock issuable to NTI common unitholders pursuant to the Merger Agreement. We urge you to read this proxy statement/prospectus, including any documents incorporated by reference and the Annexes, carefully and in its entirety. If you have any questions concerning the Merger or this proxy statement/prospectus, would like additional copies of this proxy statement/prospectus, or have questions about how to vote your NTI Common Units, please contact NTI’s proxy solicitor,                 , toll-free at [●].

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IMPORTANT NOTE ABOUT THIS PROXY STATEMENT/PROSPECTUS

This proxy statement/prospectus, which forms part of a registration statement on Form S-4 filed with the Securities and Exchange Commission (the “SEC”), constitutes a proxy statement of NTI under the Securities Exchange Act of 1934 (the “Exchange Act”) with respect to the solicitation of proxies for the special meeting of NTI Common Unitholders to, among other things, approve the Merger Proposal and the NTI Compensation Proposal. This proxy statement/prospectus is also a prospectus of WNR under the Securities Act of 1933 (the “Securities Act”) for shares of WNR Common Stock that will be issued to NTI Common Unitholders in the Merger pursuant to the Merger Agreement.

As permitted under the rules of the SEC, this proxy statement/prospectus incorporates by reference important business and financial information about WNR and NTI from other documents filed with the SEC that are not included in or delivered with this proxy statement/prospectus. Please read “Where You Can Find More Information” beginning on page 181 of this proxy statement/prospectus. You can obtain any of the documents incorporated by reference into this proxy statement/prospectus from the SEC’s website at www.sec.gov. This information is also available to you without charge upon your request in writing or by telephone to WNR or NTI at the following addresses and telephone numbers:

Western Refining, Inc.

123 W. Mills Ave., Suite 200

El Paso, Texas 79901

Attention: Jeffrey S. Beyersdorfer

Telephone: (602) 286-1530

Northern Tier Energy LP

1250 W. Washington Street, Suite 300

Tempe, Arizona 85281

Attention: Investor Relations

Telephone: (602) 302-5450

Please note that copies of the documents provided to you will not include exhibits, unless the exhibits are specifically incorporated by reference into those documents or this proxy statement/prospectus.

You may obtain certain of these documents at WNR’s website, www.wnr.com, under the “Investor Relations” section, and at NTI’s website, www.northerntier.com, under the “Investors” section. Information contained on WNR’s or NTI’s website is not incorporated by reference into this proxy statement/prospectus except as otherwise expressly stated.

You may also obtain additional copies of this proxy statement/prospectus or the documents incorporated by reference into this proxy statement/prospectus by contacting NTI’s proxy solicitor, [            ], at the address and telephone number listed below. You will not be charged for any of these documents that you request.

[[●], address, phone number]

In order to receive timely delivery of requested documents in advance of the NTI special meeting, your request should be received no later than , 2016. If you request any documents, WNR or NTI or [Proxy Solicitor] will mail them to you by first class mail or another equally prompt means within one business day after receipt of your request.

In addition, if you would like to request any documents incorporated by reference in this proxy statement/prospectus prior to deciding what merger consideration to elect, please do so at least five business days prior to the election deadline, which will be identified in the form of election provided to you in a separate mailing following the NTI special meeting.

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WNR and NTI have not authorized anyone to give any information or make any representation about the Merger, WNR or NTI that is different from, or in addition to, the information contained in this proxy statement/prospectus or in any of the materials that have been incorporated by reference into this proxy statement/prospectus. Therefore, if anyone distributes any such information, you should not rely on it. If you are in a jurisdiction where offers to exchange or sell or solicitations of offers to exchange or purchase the securities offered by this proxy statement/prospectus or the solicitation of proxies is unlawful, or if you are a person to whom it is unlawful to direct these types of activities, then the offer presented in this proxy statement/prospectus does not extend to you. The information contained in this proxy statement/prospectus speaks only as of the date of this proxy statement/prospectus or, in the case of information in a document incorporated by reference, as of the date of such document, unless the information specifically indicates that another date applies. All information in this proxy statement/prospectus concerning WNR has been furnished by WNR. All information in this proxy statement/prospectus concerning NTI has been furnished by NTI.

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QUESTIONS AND ANSWERS ABOUT THE MERGER AND THE NTI SPECIAL MEETING

Important Information and Risks. The following are brief answers to some questions that you may have regarding the Merger Proposal to be considered at the NTI Special Meeting. You should read and carefully consider the remainder of this proxy statement/prospectus, including the “Risk Factors” beginning on page 106 of this proxy statement/prospectus and the attached Annexes, because the information in this section does not provide all of the information that might be important to you. Additional important information and risk factors are also contained in the documents incorporated by reference into this proxy statement/prospectus. Please read “Where You Can Find More Information” beginning on page 181 of this proxy statement/prospectus.

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For a full list of the factors considered by the NTI GP Conflicts Committee, please see “Special Factors—Recommendation of the NTI GP Conflicts Committee and Its Reasons for Recommending Approval of the Merger Proposal and the NTI Compensation Proposal.”

The Exchange Ratios are fixed and will not be adjusted to account for any change in price of either WNR Common Stock or NTI Common Units prior to completion of the Merger. If an Exchange Ratio results in an NTI Common Unitholder being entitled to receive a fractional share of WNR Common Stock, that NTI Common Unitholder will receive cash (without interest and rounded up to the nearest whole cent) in lieu of receiving any fractional share of WNR Common Stock to which any NTI Common Unitholder would otherwise have been entitled in an amount equal to such fractional interest multiplied by the VWAP of a share of WNR Common Stock as reported on the NYSE Composite Transactions Reporting System for the 20 consecutive NYSE full trading days ending at the close of the last NYSE full trading day immediately preceding the day the Merger closes. For additional information regarding exchange procedures, please read “The Merger Agreement—Exchange of Certificates; No Fractional Units” beginning on page 126 of this proxy statement/prospectus.

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Once the Merger is completed and to the extent NTI Common Units are exchanged for WNR Common Stock, when dividends are approved and declared by WNR, former NTI Common Unitholders will receive dividends on the WNR Common Stock they receive in the Merger to the extent such unitholders continue to hold such WNR Common Stock as of the applicable record date for such dividend. For additional information, please read “Summary—Comparative Stock and Unit Prices; Comparative Dividends and Distributions” beginning on page 23 of this proxy statement/prospectus, and “The Merger Agreement—Covenants—Distributions” beginning on page 143 of this proxy statement/prospectus.

Current WNR stockholders will continue to receive dividends if, as and when declared by the WNR Board.

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Proxies received but marked as abstentions will be counted as units that are present and entitled to vote for purposes of determining the presence of a quorum. Broker non-votes (if any) will also be considered present at the NTI Special Meeting for purposes of determining the presence of a quorum but will not be included in the vote.

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Please note that you may not vote your NTI Common Units held in “street name” by returning a proxy card directly to NTI or by voting in person at the NTI Special Meeting unless you provide a “legal proxy,” which you must obtain from your broker or other nominee. If you do not instruct your broker or other nominee on how to vote your NTI Common Units, your broker or other nominee may not vote your NTI Common Units, which will have the same effect as a vote against the approval of the Merger Proposal. You should therefore provide your broker or other nominee with instructions as to how to vote your NTI Common Units.

On December 21, 2015, the NTI GP Conflicts Committee, acting on behalf of NTI GP, in its capacity as the general partner of NTI, approved the Merger Agreement and the Merger Transactions and determined that the Merger Agreement and the Merger Transactions are fair and reasonable to the NTI Unaffiliated Unitholders and NTI, and are not adverse to the interests of the NTI Unaffiliated Unitholders or the interests of NTI. The NTI GP Conflicts Committee’s approval of the Merger Agreement and the Merger Transactions constitutes “Special Approval,” as such term is defined by the NTI Partnership Agreement. The NTI GP Conflicts Committee, acting on behalf of NTI GP, in its capacity as the general partner, has directed that the Merger Agreement and the Merger Transactions be submitted to the NTI Common Unitholders at the NTI Special Meeting for approval. The NTI GP Conflicts Committee recommends that the NTI Common Unitholders vote in favor of the Merger Proposal and the NTI Compensation Proposal.

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Your presence without voting at the NTI Special Meeting will not automatically revoke your proxy. Beneficial holders who hold their NTI Common Units in “street name” by a broker or other nominee may revoke their proxy by following the instructions provided by such broker or nominee.

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For more details on the election procedures, see “Special Factors—NTI Common Unitholders Making Elections.”

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If you do not make a valid election with respect to any NTI Common Units you own of record, you will receive written instructions from the exchange agent after completion of the proposed transactions on how to exchange your NTI Common Units for the Merger Consideration.

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SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This proxy statement/prospectus and the documents WNR and NTI have incorporated herein by reference contain various forward-looking statements and information that reflect WNR’s and/or NTI’s current beliefs, expectations or intentions regarding future events. These forward-looking statements may be identified by the use of words such as “may,” “will,” “could,” “should,” “would,” “expect,” “plan,” “project,” “intend,” “anticipate,” “believe,” “estimate,” “forecast,” “predict,” “potential,” “pursue,” “target,” “continue,” “contemplate” and similar expressions that contemplate future events. These statements appear in a number of places in this proxy statement/prospectus and in the documents incorporated by reference.

All statements other than statements of historical fact included or incorporated by reference in this proxy statement/prospectus, including statements regarding WNR’s and/or NTI’s financial position, business strategy and other plans and objectives for future operations (including management of the combined company) or transactions, and statements regarding the approval of the Merger Agreement and the Merger Transactions, the satisfaction of the closing conditions to the Merger, the timing of the completion of the Merger, WNR’s ability to obtain financing for the Merger, expected U.S. federal income tax consequences, expectations and intentions regarding outstanding litigation, expectations with respect to the synergies, including (i) increased scale, asset diversity and competitiveness and (ii) financial and operational synergies, costs and other anticipated effects of the Merger and expectations regarding future dividends paid to holders of WNR Common Stock, are forward-looking statements.

Although WNR and NTI believe that such forward-looking statements are based on reasonable assumptions, neither WNR nor NTI gives any assurance that such expectations will in fact occur. Certain factors could cause actual results to differ materially from those in the forward-looking statements. Such factors include, but are not limited to:

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WNR and NTI caution that the foregoing list of factors is not exclusive. Additional information concerning these and other risk factors is contained in WNR’s and NTI’s most recently filed Annual Reports on Form 10-K, subsequent Quarterly Reports on Form 10-Q, recent Current Reports on Form 8-K and other SEC filings. In addition, WNR and NTI may be subject to currently unforeseen risks that may have a materially adverse effect on them. All subsequent written and oral forward-looking statements concerning WNR, NTI, the proposed Merger and other Merger Transactions, or other matters attributable to WNR or NTI or any person acting on their behalf are expressly qualified in their entirety by the cautionary statements above. The forward-looking statements speak only as of the date made and, other than as required by law, neither WNR nor NTI undertakes any obligation to update publicly or revise any of these forward-looking statements, whether as a result of new information, future events or otherwise.

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SPECIAL FACTORS

Effects of the Merger

Pursuant to the Merger Agreement, WNR will acquire all of the outstanding NTI Common Units that WNR and its subsidiaries do not already own. For purposes of this proxy statement/prospectus, references to subsidiaries of WNR do not include NTI and its subsidiaries unless otherwise indicated. At the Effective Time of the Merger, MergerCo, an indirect wholly-owned subsidiary of WNR, will merge with and into NTI with NTI surviving the Merger as an indirect wholly-owned subsidiary of WNR, and each outstanding NTI Common Unit, other than those NTI Common Units owned by WNR or any of its subsidiaries, will be converted into the right to receive, at the election of the unitholder, either (i) a combination of $15.00 in cash without interest and 0.2986 of a share of WNR Common Stock, or (ii) $26.06 in cash without interest or (iii) 0.7036 of a share of WNR Common Stock. The Cash Election and Stock Election, however, will be subject to proration to ensure that the total amount of cash paid and the total number of shares of WNR Common Stock issued in the Merger to NTI Public Unitholders as a whole are equal to the total amount of cash and number of shares of WNR Common Stock that would have been paid and delivered if all NTI Public Unitholders received the Standard Mix of Consideration.

All of the limited liability company interests in MergerCo outstanding immediately prior to the Effective Time, which are currently held by MergerCo HoldCo, will automatically be converted into, in the aggregate, the number of NTI Common Units (excluding any NTI Common Units owned by WNR or any of its subsidiaries) issued and outstanding immediately prior to the Effective Time. All NTI Common Units owned by WNR or any of its subsidiaries immediately prior to the Effective Time will be unchanged and remain issued and outstanding as NTI Common Units of the surviving entity at the Effective Time. Immediately after the Effective Time, the NTI Common Units resulting from the conversion of the limited liability company interests in MergerCo and the NTI Common Units owned by WNR or its subsidiaries immediately prior to the Effective Time will constitute all of the issued and outstanding common units of, and limited partnership interests in, the surviving entity. Consequently, MergerCo HoldCo, a wholly-owned subsidiary of NT InterHoldCo and the sole member of MergerCo, and NT InterHoldCo, a wholly-owned subsidiary of WNR and direct holder of the NTI Common Units owned by WNR or its subsidiaries immediately prior to the Effective Time, will jointly own all of the limited partner interests in the surviving entity. The general partner interest in NTI issued and outstanding immediately prior to the Effective Time will be unchanged and remain issued and outstanding in the surviving entity, and NTI GP, as the holder of such general partner interest, will continue as the sole general partner of the surviving entity as set forth in NTI’s Partnership Agreement (which will continue unchanged as the agreement of limited partnership of the surviving entity as of the Effective Time).

Based on the VWAP of a share of WNR Common Stock for the 20 consecutive NYSE full trading days ending at the close of regular trading hours on the NYSE on October 23, 2015 (the last trading day before the announcement of WNR’s proposal to acquire all of the outstanding NTI Common Units owned by the public), the Merger Consideration represents a premium of approximately 18% above the VWAP of the NTI Common Units for the same period.

The Merger Agreement is included as an exhibit to the registration statement of which this proxy statement/prospectus is a part. The discussion in this proxy statement/prospectus of the Merger and the material terms of the Merger Agreement is subject to, and is qualified in its entirety by reference to, the Merger Agreement, a copy of which is attached as Annex A to this proxy statement/prospectus and incorporated by reference herein.

Background of the Merger

On November 12, 2013, WNR acquired from ACON Refining Partners L.L.C. and TPG Refining L.P. all of the equity interests in NT InterHoldCo, a Delaware limited liability company, which held approximately 38.7% of the limited partner interests in NTI and 100% of the equity interests in NTI GP, for total consideration of $775 million

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plus the distribution on the NTI Common Units acquired with respect to the quarter ended September 30, 2013. As a result of this transaction, which we refer to as the “Sponsor Acquisition,” WNR acquired indirect ownership of 100% of NTI GP and approximately 38.7% of the then outstanding NTI Common Units.

Among other things, as the indirect sole member of NTI GP, WNR gained the exclusive right to appoint directors to the NTI GP Board. In connection with the closing of the Sponsor Acquisition, WNR accepted the resignations of the NTI GP directors affiliated with ACON Refining Partners L.L.C. and TPG Refining L.P. and appointed to the NTI GP Board four WNR officers. The WNR officers appointed as board members of NTI GP were: Paul L. Foster, Jeff A. Stevens, Scott D. Weaver and Lowry Barfield. Paul L. Foster is the Chairman of the WNR Board and Executive Chairman of WNR and the Chairman of the NTI GP Board. Jeff A. Stevens is a director of WNR, President and Chief Executive Officer of WNR and a director of NTI GP. Scott D. Weaver is a director and Vice President, Assistant Treasurer, of WNR, and a director of NTI GP. Lowry Barfield is the General Counsel of WNR and a director of NTI GP.

Three then-existing independent members of the NTI GP Board continued to serve as directors of NTI GP following the Sponsor Acquisition. These independent directors are Rocky Duckworth, Thomas Hofmann and Dan F. Smith. In January 2014, NT InterHoldCo appointed Timothy Bennett to the NTI GP Board as a fourth independent director. In April 2014, NT InterHoldCo appointed David L. Lamp, the President and Chief Executive Officer of NTI GP, to the NTI GP Board.

The WNR Board from time to time reviews and evaluates potential strategic alternatives with WNR management, including possible acquisitions, dispositions and business combination transactions, and since the consummation of the Sponsor Acquisition, the WNR Board has, from time to time, considered a wide variety of potential strategic alternatives involving both WNR and NTI, including dispositions of assets to NTI and acquisitions of refinery assets from third parties jointly with NTI, some of which transactions were preliminarily discussed and evaluated with NTI, with a goal of utilizing the unique corporate structure of WNR and NTI to maximize value for stockholders of WNR over the long-term. However, the evaluation of such transactions never progressed beyond a preliminary stage.

In 2015, WNR management began to focus its analysis on two potential strategic alternatives involving WNR and NTI: (i) the acquisition by WNR of all of the outstanding NTI Common Units not already held by WNR and its subsidiaries and (ii) a transaction involving the sale of WNR’s refining assets to NTI. WNR management was analyzing whether either transaction, each of which would result in one entity holding all of WNR’s and NTI’s refining assets, would provide key benefits, including an entity with a diversified asset base, enhanced credit ratings and increased scale. During this time, WNR management also engaged Davis Polk & Wardwell LLP and Vinson & Elkins, as legal counsel, to assist in the evaluation of the strategic alternatives.

On October 16, 2015, at a special meeting of the WNR Board, WNR management presented to the WNR Board an overview of the two strategic alternatives management had been analyzing, including WNR management’s analysis of the benefits and detriments of each alternative relative to each other and the status quo, and preliminary illustrative valuation comparisons, which materials were prepared with the assistance of Goldman Sachs. The meeting was also attended by representatives of Goldman Sachs. During the meeting, the WNR Board authorized WNR management to proceed with further analysis on a potential acquisition by WNR of all of the outstanding NTI Common Units not already held by WNR and its subsidiaries, and to make a recommendation to the WNR Board regarding whether to proceed with such a transaction, and if so, on what terms.

On October 22, 2015, the WNR Board convened a special meeting of the WNR Board, to further consider a potential acquisition by WNR of all of the outstanding NTI Common Units not held by WNR and its subsidiaries. During the meeting, the WNR Board and WNR management discussed several potential benefits of the potential transaction, including that it would simplify WNR’s corporate structure, would provide the combined company

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with better access to the capital markets, would make it easier for the analyst and investor community to understand WNR’s capital structure and would make it easier for WNR to manage working capital and growth capital projects, without the limitations created by NTI’s variable distribution master limited partnership model. The WNR Board also discussed the key components of any offer it might make to acquire all of the outstanding NTI Common Units not held by WNR and its subsidiaries, including the economic terms of the offer, and WNR management presented materials analyzing the potential transaction, which materials were prepared with the assistance of Goldman Sachs. The meeting was also attended by representatives of Goldman Sachs. At the conclusion of the meeting, the WNR Board authorized the delivery by WNR to the NTI GP Conflicts Committee of an offer to acquire all of the outstanding NTI Common Units not owned by WNR and its subsidiaries for consideration per unit of $17.50 in cash and 0.2266 of a share of WNR Common Stock that would together imply consideration equal to a 15% premium to NTI’s trading price, utilizing the 20-day VWAP for shares of WNR Common Stock and NTI Common Units as of October 23, 2015.

Later on October 22, 2015, following the WNR Board special meeting, Jeff A. Stevens told David L. Lamp and David L. Lamp later advised Mr. Duckworth, as the Chairman of the NTI GP Conflicts Committee, that there was a likelihood that WNR would propose a transaction involving WNR and NTI. Mr. Duckworth subsequently informed the other members of the NTI GP Conflicts Committee and Akin Gump that WNR may be proposing a transaction involving WNR and NTI. The NTI GP Conflicts Committee had previously engaged Akin Gump in September 2015 to serve as the committee’s independent legal counsel in connection with the committee’s consideration of potential future transactions involving NTI and WNR and/or WNRL.

On the evening of October 23, 2015, WNR delivered to Messrs. Duckworth, Bennett, Hofmann and Smith, as the members of the NTI GP Conflicts Committee, a letter setting forth a proposal for WNR to acquire all of the outstanding NTI Common Units not owned by WNR for consideration equal to $17.50 in cash and 0.2266 of a share of WNR Common Stock for each issued and outstanding publicly-held NTI Common Unit, subject to the negotiation and execution of mutually acceptable definitive documentation (the “October 23 Proposal”). The October 23 Proposal implied a 15% premium to the 20-day VWAP of the NTI Common Unit price as of October 23, 2015, and represented aggregate consideration of $27.62 per NTI Common Unit based on the 20-day VWAPs for NTI Common Units and WNR Common Stock as of October 23, 2015. The letter containing the October 23 Proposal also stated that (i) WNR anticipated the NTI GP Board would delegate the authority to evaluate and respond to the October 23 Proposal to the NTI GP Conflicts Committee and (ii) that WNR was only interested in acquiring NTI Common Units and had no interest in selling any of its interests in NTI, selling assets to NTI or pursuing other strategic alternatives involving NTI.

During the afternoon of October 25, 2015, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Akin Gump and certain members of NTI management. The committee and Akin Gump discussed the October 23 Proposal at a high level, the anticipated process for the committee to review and consider the proposal, and the process to be conducted to select the committee’s independent financial advisor, including potential candidates to interview. NTI management then reviewed with the committee drafts of the current report on Form 8-K and press release relating to the October 23 Proposal to be filed and issued by NTI the following day.

On the morning of October 26, 2015, each of WNR and NTI issued a press release announcing the delivery and receipt of the October 23 Proposal, and WNR filed an amendment to its Schedule 13D with respect to the NTI Common Units indirectly owned by WNR, reflecting the delivery of the October 23 Proposal.

On October 26, 2015, WNR formally engaged Goldman Sachs as its financial advisor with respect to a potential acquisition by WNR of all of the outstanding NTI Common Units not held by WNR and its subsidiaries, as well as other potential strategic alternatives.

During the morning of October 28, 2015, certain members of the NTI GP Conflicts Committee held an in-person meeting in Houston, Texas. Representatives of Akin Gump were present at the meeting during which the

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committee members in attendance interviewed three investment banks identified as candidates to serve as independent financial advisor to the NTI GP Conflicts Committee, including Evercore. At that meeting, representatives of Evercore provided an overview of Evercore, including the firm’s experience with mergers and acquisitions involving master limited partnerships and its experience advising conflicts committees in connection with such transactions. The representatives of Evercore also provided information regarding Evercore’s service as independent financial advisor to the conflicts committee of the board of directors of the general partner of WNRL. Following the interviews, the committee members in attendance discussed their initial impressions regarding each of the three firms.

On October 28, 2015, Vinson & Elkins distributed to Akin Gump draft resolutions of the NTI GP Board authorizing the NTI GP Conflicts Committee with respect to its evaluation of the October 23 Proposal. From October 28 through October 30, 2015, Vinson & Elkins and Richards, Layton & Finger on the one hand, and Akin Gump, on the other hand, exchanged multiple drafts of the proposed authorizing resolutions.

During the morning of October 29, 2015, members of the NTI GP Conflicts Committee and a representative of Akin Gump held a telephonic meeting to interview a fourth candidate to serve as the committee’s independent financial advisor. Following the interview, the committee members in attendance discussed their initial impressions regarding the firm.

On October 30, 2015, following further discussions among the members of the NTI GP Conflicts Committee, the committee determined to select Evercore as its independent financial advisor, subject to the negotiation of a mutually acceptable engagement letter.

During the morning of November 5, 2015, the NTI GP Conflicts Committee held a telephonic meeting at which members of WNR’s management team gave a presentation to the committee regarding the October 23 Proposal. Attendees included the NTI GP Conflicts Committee, members of WNR’s management team, members of NTI’s management team, and representatives of Evercore, Akin Gump and Vinson & Elkins. During the meeting, WNR management reviewed with the members of the NTI GP Conflicts Committee what they believed to be the key benefits of the proposed transaction to NTI Common Unitholders and to all WNR stockholders following completion of a merger, discussed the structure and terms of the October 23 Proposal, and presented certain pro forma valuation information. The WNR management presentation was provided to the NTI GP Conflicts Committee and its advisors on November 4, 2015, and to NTI management on November 5, 2015, and included certain preliminary summary financial projections for WNR on a pro forma basis for the Proposed Transaction, for WNR on a deconsolidated basis, for NTI on a standalone basis, and for WNRL on a standalone basis. During the course of the meeting, members of the NTI GP Conflicts Committee and representatives of Evercore and Akin Gump asked questions regarding the October 23 Proposal and the potential pro forma combined company generally that were responded to by members of WNR management. Following the WNR presentation, the NTI GP Conflicts Committee met on a separate call with representatives from Evercore and Akin Gump during which they discussed their initial impressions of the proposal and the proposed transaction.

During the afternoon of November 5, 2015, representatives of Evercore, Akin Gump and NTI management held a conference call to discuss due diligence questions posed by Evercore regarding the preliminary NTI standalone summary financial projections included in the WNR management materials presented at the meeting earlier that day, and the request of the NTI GP Conflicts Committee to set up a due diligence meeting with NTI management to discuss the NTI projections provided by WNR management. Later on November 5, 2015, at the request of the NTI GP Conflicts Committee and Evercore, NTI management provided a copy of the approved NTI budget for 2016 to Akin Gump, who then circulated copies of the budget to the NTI GP Conflicts Committee and representatives of Evercore. Later that day, Evercore contacted WNR management in order to commence the coordination of Evercore’s due diligence requests and request access to WNR’s virtual data room.

During the afternoon of November 6, 2015, the Nominating and Governance Committee of the NTI GP Board held a telephonic meeting. At the meeting, the Nominating and Governance Committee determined, and

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recommended that the NTI GP Board determine, that: (i) none of the members of the NTI GP Conflicts Committee is an officer or employee of NTI GP or any of its affiliates or holds any ownership interests in NTI GP, its affiliates, NTI or any subsidiaries of NTI, other than common units, PIK common units or interests in NTI granted under NTI’s long-term incentive plan; (ii) each of the members of the NTI GP Conflicts Committee meets the independence standards required to serve on an audit committee of a board of directors by the Exchange Act and the listing standards of the NYSE, and none of the members of the NTI GP Conflicts Committee has any material relationship with NTI, NTI GP or any of their affiliates; and (iii) none of the members of the NTI GP Conflicts Committee has any relationship or interests that would interfere with the exercise of his independent judgment in carrying out the responsibilities of a director of NTI GP or a member of the NTI GP Conflicts Committee or would otherwise disqualify him from serving as a member of the NTI GP Conflicts Committee.

During the afternoon of November 6, 2015, the NTI GP Board held a special telephonic meeting. During the meeting, the NTI GP Board unanimously determined that each of the members of the NTI GP Conflicts Committees continued to satisfy the requirements for serving on the NTI GP Conflicts Committee, including the requirement that all members of the NTI GP Conflicts Committee be independent, and formally delegated to the NTI GP Conflicts Committee the full power, authority and responsibilities of the NTI GP Board to the extent necessary to do the following: (i) to review and evaluate the terms and conditions of the October 23 Proposal and any other agreements or arrangements necessary to effect the potential transaction or incidental thereto, and including any changes to the terms of the October 23 Proposal as negotiated by WNR and the NTI GP Conflicts Committee (referred to as the “Proposed Transaction”) on behalf of NTI GP, NTI and the NTI Unaffiliated Unitholders; (ii) to negotiate, or delegate to any person or persons the ability to negotiate, the terms and conditions of the Proposed Transaction, including the consideration to be received by the NTI Common Unitholders therein; (iii) to determine whether or not to grant Special Approval pursuant to Section 7.9 of the NTI Partnership Agreement with respect to the Proposed Transaction (with the NTI GP Conflicts Committee having the full power and authority of the NTI GP Board, acting for and on behalf of NTI GP (in its capacity as general partner of NTI), to approve or not approve the Proposed Transaction without the necessity of any additional approval of the full NTI GP Board, but having no authority to approve or accept any potential alternative transaction to the Proposed Transaction); (iv) to make any recommendation to the NTI Unaffiliated Unitholders regarding what action, if any, should be taken by the NTI Unaffiliated Unitholders with respect to the Proposed Transaction; and (v) if applicable and as appropriate, to exercise the full authority of the NTI GP Board with respect to the approval of the Proposed Transaction and the transactions contemplated thereby, and the authorization of the execution and delivery of any documents, instruments or agreements with respect thereto.

On November 6, 2015, WNR made available to the NTI GP Conflicts Committee and its advisors a virtual data room. On November 7, 2015, WNR uploaded an updated set of preliminary financial projections to the virtual data room.

On November 10, 2015, Evercore submitted initial due diligence questions to WNR management.

On November 10, 2015, the NTI GP Conflicts Committee held an in-person meeting in Houston, Texas with members of NTI management and representatives of Evercore and Akin Gump. At the meeting, at the request of the NTI GP Conflicts Committee, members of NTI management discussed with the NTI GP Conflicts Committee their assessment of the NTI projections included in the materials previously provided by WNR, and responded to due diligence questions asked by the NTI GP Conflicts Committee and representatives of Evercore and Akin Gump. Representatives of Akin Gump also gave a presentation to the committee members regarding the NTI Partnership Agreement and the duties of the committee under that agreement in connection with its review and consideration of the Proposed Transaction.

On the afternoon of November 10, 2015, Evercore submitted additional due diligence requests to WNR management, including a request for WNR to run and provide a sensitivity case for the standalone and pro forma financial projections provided by WNR management using historical five-year average crack spreads for both WNR and NTI.

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On the afternoon of November 11, 2015, members of WNR management and NTI management and representatives of Goldman Sachs, Vinson & Elkins, Evercore and Akin Gump held a conference call to discuss due diligence questions posed by Evercore regarding the preliminary financial projections provided by WNR management.

On the afternoon of November 12, 2015, members of WNR management and NTI management, and representatives of Goldman Sachs, Vinson & Elkins, Evercore and Akin Gump held a conference call to discuss additional due diligence questions posed by Evercore regarding the preliminary financial projections provided by WNR management.

On November 13, 2015, Vinson & Elkins, as counsel to WNR, delivered an initial draft of the Merger Agreement to Akin Gump. The draft of the Merger Agreement was consistent with the October 23 Proposal and provided for aggregate consideration per NTI Common Unit of $17.50 in cash and 0.2266 of a share of WNR Common Stock.

On November 15, 2015, representatives of Evercore submitted a supplemental due diligence request for certain financial information to WNR.

On November 16, 2015, WNR and NTI exchanged a fully-executed copy of a confidentiality agreement between WNR and NTI dated November 11, 2015.

On November 17, 2015, Akin Gump submitted a due diligence request list with respect to legal matters to Vinson & Elkins.

On the afternoon of November 17, 2015, members of WNR management and representatives of Goldman Sachs, Vinson & Elkins, Evercore and Akin Gump held a conference call to discuss due diligence questions posed by Evercore regarding the preliminary financial projections provided by WNR management.

On the morning of November 18, 2015, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Akin Gump, who provided the committee with an update regarding the current status of various matters, including due diligence efforts by Evercore and Akin Gump, and Akin Gump’s review of the initial draft of the Merger Agreement provided by Vinson & Elkins. At the meeting, the NTI GP Conflicts Committee (i) approved and ratified the engagement of Evercore as the committee’s independent financial advisor, including the final version of the Evercore engagement letter dated November 12, 2015; and (ii) authorized Akin Gump to proceed with the engagement of Morris Nichols as the committee’s independent Delaware legal counsel.

On November 20, 2015, NTI management provided to the Chairman of the NTI GP Conflicts Committee copies of letters that had been received to date by NTI from NTI Common Unitholders and directed to the NTI GP Board relating to the October 23 Proposal, which the Chairman subsequently distributed to the other members of the committee and Evercore and Akin Gump.

On November 21, 2015, WNR uploaded an updated set of preliminary financial projections to the virtual data room.

On November 23, 2015, Evercore submitted a supplemental due diligence request for certain financial information to WNR.

On the afternoon of November 23, 2015, members of NTI management and Akin Gump held a conference call to discuss certain terms contained in the initial draft of the Merger Agreement, including the representations to be made by NTI, the operating covenants applicable to NTI, and terms regarding NTI employee matters.

On November 25, 2015, Akin Gump provided the NTI GP Conflicts Committee with a revised draft of the Merger Agreement that included proposed revisions for the committee’s consideration.

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On November 30, 2015, WNR uploaded an updated set of preliminary financial projections to the virtual data room.

On the morning of December 1, 2015, the NTI GP Conflicts Committee and representatives of Evercore and Akin Gump held an in-person meeting in Houston, Texas. At the meeting, representatives of Evercore discussed with the committee the due diligence that had been conducted to date and the related impact on the preliminary financial projections provided by WNR management, and Evercore’s preliminary financial analysis of the Proposed Transaction, based on the preliminary financial projections received from WNR to date, and noting that certain items were subject to change pending receipt of WNR’s final set of projections. During the presentation Evercore provided, among other things: (i) a summary of the terms of the Proposed Transaction; (ii) a situational overview for NTI, including the financial projections for NTI provided by WNR management; (iii) a detailed financial analysis of NTI, including a discounted cash flow analysis, a precedent transactions analysis, a peer group trading analysis, and a premiums paid analysis; (iv) a situational overview for WNR and WNRL, including the financial projections for WNR and WNRL provided by WNR management; (v) an indicative valuation analysis for the proposed consideration to be received by the NTI Unaffiliated Unitholders in the Proposed Transaction; and (vi) an analysis of WNR on a pro forma basis for the Proposed Transaction. During the presentation, the NTI GP Conflicts Committee asked, and representatives of Evercore answered, questions with respect to Evercore’s financial analysis. Following the presentation, the NTI GP Conflicts Committee and its advisors engaged in a discussion regarding a potential counterproposal to the October 23 Proposal. Following the discussion, the NTI GP Conflicts Committee unanimously directed Evercore to deliver a counterproposal to WNR management that included the following terms: (A) an increase of the exchange ratio for the WNR Common Stock component of the merger consideration from 0.2266 of a share of WNR Common Stock to 0.2750 of a share of WNR Common Stock per NTI Common Unit, while maintaining the proposed cash consideration of $17.50 per NTI Common Unit; (B) a request that NTI would continue to make quarterly cash distributions on its outstanding common units in the ordinary course, and NTI would make a final distribution pro-rated for the period commencing on the first day of the quarter in which the Merger Transaction closes through the Closing Date of the Merger; (C) a request that NTI Common Unitholders would have the right to elect to receive either all cash, all WNR Common Stock, or cash and WNR Common Stock, as merger consideration, subject to proration (the “Consideration Election Term”); and (D) a statement that the NTI GP Conflicts Committee was still considering whether to seek a term requiring the Proposed Transaction to be approved by a majority of the NTI Unaffiliated Unitholders, depending upon WNR’s response to the committee’s counterproposal (collectively, the “December 1 Counterproposal”).

On the afternoon of December 1, 2015, a representative of Evercore delivered the December 1 Counterproposal to WNR management.

On December 2, 2015, WNR uploaded the final version of the financial projections prepared by WNR management to the virtual data room, which are referred to in this proxy statement/prospectus as the “Management Projections” and are described under “Special Factors—Projected Financial Information.”

On December 3, 2015, a representative of Goldman Sachs contacted a representative of Evercore to inform Evercore that the WNR Board was planning to hold a special meeting on December 7, 2015 to consider the December 1 Counterproposal.

On December 4, 2015, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Evercore, Akin Gump and Morris Nichols to review and consider the terms of the draft Merger Agreement provided by Vinson & Elkins. Representatives of Akin Gump (i) provided the NTI GP Conflicts Committee with an overview of the terms of the initial draft of the Merger Agreement; and (ii) discussed with the committee a number of potential negotiation points and recommended changes to the Merger Agreement, including: (A) a covenant obligation under which WNR must vote its NTI Common Units in favor of the Proposed Transaction; (B) a “standstill” term prohibiting WNR from acquiring additional NTI Common Units; (C) a broadening of the NTI GP Conflicts Committee’s authority to change its recommendation with respect to the Proposed Transaction

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between the signing of the Merger Agreement and the date of the NTI Special Meeting to approve the Proposed Transaction; (D) removing any obligation of NTI to pay a termination fee to WNR as contemplated by the initial draft of the Merger Agreement; and (E) adding a covenant that WNR will not change the composition or authority of the NTI GP Conflicts Committee between the signing of the Merger Agreement and the closing of the Proposed Transaction. During the course of the meeting, the NTI GP Conflicts Committee asked, and representatives of Akin Gump and Morris Nichols answered, questions with respect to the draft Merger Agreement. Following the discussions, the NTI GP Conflicts Committee directed Akin Gump to provide a revised draft of the Merger Agreement to Vinson & Elkins. Later that day, Akin Gump provided a revised draft of the Merger Agreement to Vinson & Elkins reflecting the revisions discussed with, and approved by, the committee.

On December 7, 2015, the WNR Board held a meeting during which the WNR Board considered the NTI counterproposal and WNR management’s analysis and recommendations regarding a proposed response, with the participation of representatives of Goldman Sachs. Following the meeting, WNR delivered a counterproposal to representatives of Evercore, on behalf of the NTI GP Conflicts Committee, under which the merger consideration per NTI Common Unit would be modified from the October 23 Proposal to consist of $15.00 in cash and 0.2986 of a share of WNR Common Stock (the “December 7 Counterproposal”). As part of its counterproposal, WNR stated that: (i) it would be sending an analysis that suggested higher implied pro forma share/unit prices; (ii) it agreed to the Consideration Election Term proposed by the NTI GP Conflicts Committee; (iii) it agreed that NTI should pay a pro rata distribution to the NTI Common Unitholders based on the beginning of the quarter in which the closing occurs to the effective date of the Merger; (iv) it requested that the NTI GP Conflicts Committee provide more clarity regarding its thoughts on the proposed term requiring approval of the Proposed Transaction by a majority of the NTI Unaffiliated Unitholders; (v) the counterproposal was WNR’s “best and final” offer; and (vi) it requested a response from the NTI GP Conflicts Committee by December 14, 2015.

On the morning of December 9, 2015, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Evercore, Akin Gump and Morris Nichols to discuss the December 7 Counterproposal. At the meeting, representatives of Evercore reviewed the counterproposal with the committee, and provided the committee with: (i) an updated valuation of NTI; (ii) an updated valuation of the proposed consideration to the NTI Unaffiliated Unitholders; (iii) an updated review of the pro forma impact of the Proposed Transaction to the NTI Unaffiliated Unitholders; and (iv) an explanation of the items that had changed in Evercore’s presentation since the meeting held on December 1, 2015. During the presentation, the NTI GP Conflicts Committee asked, and representatives of Evercore answered, questions with respect to Evercore’s financial analysis. Following the presentation, the NTI GP Conflicts Committee and its advisors engaged in a discussion regarding a potential counterproposal to the December 7 Counterproposal under which the committee would seek an increase of the amount of the cash component of the merger consideration payable per NTI common unit from $15.00 per unit to $15.50 per unit. The NTI GP Conflicts Committee and its advisors also discussed the potential implications of WNR’s assertion that its current counterproposal was its “best and final” offer.

On the morning of December 10, 2015, a representative of Vinson & Elkins telephoned a representative of Akin Gump and communicated that WNR planned to wait to respond to Akin Gump’s markup of the draft Merger Agreement until after WNR had received a response from the NTI GP Conflicts Committee to the December 7 Counterproposal, and Akin Gump subsequently informed the NTI GP Conflicts Committee, Evercore and Morris Nichols of this conversation.

On the morning of December 14, 2015, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Evercore, Akin Gump and Morris Nichols. At the meeting, the NTI GP Conflicts Committee and its advisors discussed the recent declines in WNR’s Common Stock price and NTI’s Common Unit price and the implications thereof to the Proposed Transaction. Representatives of Evercore provided the Committee with an updated analysis of the December 7 Counterproposal, giving effect to the closing prices for WNR Common Stock and NTI Common Units as of December 11, 2015. Following a discussion with its advisors, the NTI GP Conflicts Committee directed Evercore to relay a counterproposal to WNR management, on behalf of the

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committee, under which the proposed cash component of the merger consideration would be increased from $15.00 per NTI Common Unit to $16.00 per NTI Common Unit (the “December 14 Counterproposal”).

Following the Committee meeting on December 14, 2015, representatives of Evercore communicated the December 14 Counterproposal to WNR management.

On December 15, 2015, Paul Foster, Chairman of the WNR Board, telephoned Rocky Duckworth, the Chairman of the NTI GP Conflicts Committee, and communicated that the December 7 Counterproposal was in fact WNR’s “best and final” offer and that Mr. Foster intended to recommend the withdrawal of WNR’s merger proposal at 5:00 p.m., Phoenix, Arizona time, on December 17, 2015 unless the NTI GP Conflicts Committee agreed to the economic terms of WNR’s “best and final” offer. Mr. Foster subsequently provided a written letter to Mr. Duckworth confirming the points communicated in their conversation.

Later in the day on December 15, 2015, Mr. Duckworth telephoned Mr. Foster and requested an extension of the deadline to respond to the December 7 Counterproposal to 5:00 p.m., Phoenix, Arizona time, on December 18, 2015, to which Mr. Foster agreed.

On December 16, 2015, Mr. Duckworth received a letter from Jeff Stevens, WNR’s President and Chief Executive Officer, confirming that WNR had extended the deadline to respond to its proposal to 5:00 p.m., Phoenix, Arizona time, on December 18, 2015.

On the evening of December 16, 2015, Vinson & Elkins delivered a revised draft of the Merger Agreement to Akin Gump.

On the morning of December 17, 2015, a representative of Vinson & Elkins telephoned a representative of Akin Gump and communicated that WNR would not be willing to agree to a term requiring the Proposed Transaction to be approved by a majority of the NTI Unaffiliated Unitholders.

On the morning of December 17, 2015, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Evercore, Akin Gump and Morris Nichols. At the meeting, the NTI GP Conflicts Committee and its advisors discussed WNR’s response to the December 14 Counterproposal, and Evercore provided the committee with a comparison of the October 23 Proposal, the December 1 Counterproposal and the December 7 Counterproposal using various unit and share prices and updated for the December 16, 2015 closing price for WNR Common Stock of $37.88 per share. During Evercore’s presentation, the NTI GP Conflicts Committee asked whether or not the public market price for NTI Common Units had been supported during the recent stock market decline in the energy sector by the October 23 Proposal, and what might happen to the trading price of NTI Common Units if the committee rejected the December 7 Counterproposal. In responding to the committee’s questions, Evercore discussed a case study of NGL Energy Partners LP’s failed offer to acquire TransMontaigne Partnership L.P. (“TransMontaigne”), including how TransMontaigne’s units traded following TransMontaigne’s rejection of the offer. Following the discussion, the NTI GP Conflicts Committee unanimously determined to accept the economic terms of the December 7 Counterproposal, subject to negotiation of a mutually acceptable merger agreement and receipt of a fairness opinion from Evercore. Akin Gump then provided the NTI GP Conflicts Committee with an update regarding the current status of the Merger Agreement negotiations, including the changes reflected in the revised draft of the Merger Agreement received from Vinson & Elkins on December 16, 2015, noting: (i) that the cash distribution terms needed to be developed further in order to, among other things, address the payment of cash distributions with respect to periods following the first quarter of 2016 in the event the Merger were to close after the first quarter of 2016; (ii) that WNR had accepted the NTI GP Conflicts Committee’s request to remove any requirement for NTI to pay a termination fee; and (iii) that in lieu of a termination fee, WNR was seeking to require NTI to be subject to certain expense reimbursement obligations following a termination of the Merger Agreement. Akin Gump also noted that Vinson & Elkins had telephoned earlier in the day to communicate that WNR would not be willing to agree to a term requiring the Proposed Transaction to be approved by a majority of the NTI Unaffiliated Unitholders. Following the

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discussion, the NTI GP Conflicts Committee determined not to pursue a term requiring the Proposed Transaction to be approved by a majority of the NTI Unaffiliated Unitholders after considering the economic terms of the Proposed Transaction, the NTI GP Conflicts Committee’s ability to change its recommendation, and WNR’s stated position that it would not agree to such a term. The committee then directed Akin Gump to work with Vinson & Elkins to finalize the terms of the Merger Agreement, including the cash distribution terms, and to propose a cap on NTI’s expense reimbursement obligations in the event WNR terminated the Merger Agreement following a change in recommendation by the NTI GP Conflicts Committee. Mr. Duckworth then directed Evercore and Akin Gump to contact WNR and Vinson & Elkins, respectively, in order to communicate the points discussed at the meeting. Mr. Duckworth also advised the NTI GP Conflicts Committee that he would call Mr. Foster to communicate that the committee had agreed to accept the economic terms of the December 7 Counterproposal, subject to negotiation of a mutually acceptable Merger Agreement and receipt of a fairness opinion from Evercore, and to express the committee’s strongly held view that the NTI Unaffiliated Unitholders should receive a pro rata cash distribution with respect to the quarter in which the transaction closes.

Later on the morning of December 17, 2015, Mr. Duckworth telephoned Mr. Foster and advised him that (i) the NTI GP Conflicts Committee had agreed to the principal economic terms of the December 7 Counterproposal, subject to negotiation of a mutually acceptable Merger Agreement and final approval by the committee following receipt of Evercore’s final financial analysis and fairness opinion; (ii) the committee requested that the NTI Common Unitholders receive a pro rata cash distribution relating to NTI’s operations through the closing of the Merger, accepting that reasonable estimates may need to be made; and (iii) Evercore and Akin Gump would be in contact with WNR management and Vinson & Elkins, respectively, to discuss the proposed Merger Agreement, and timing and process matters.

On the afternoon of December 17, 2015, Mr. Foster telephoned Mr. Duckworth and stated that (i) WNR had agreed in principal to the NTI GP Conflicts Committee’s views regarding the payment of a pro rata distribution for the quarter in which the transaction closed; (ii) WNR management and Vinson & Elkins would work with Evercore and Akin Gump regarding the mechanics for determining the requested pro rata cash distribution; and (iii) WNR was planning to schedule a special meeting of the WNR Board on December 21, 2015 to finalize their approval of the Proposed Transaction.

On December 17, 2015, representatives of Evercore and WNR management discussed the pro rata cash distribution mechanics, and on the evening of December 17, 2015, Vinson & Elkins provided Akin Gump with an example of the pro rata cash distribution determination mechanics outlining the interrelationship between the closing date for the Proposed Transaction and the rights of the NTI Unaffiliated Unitholders to receive either a pro rata cash distribution from NTI or a WNR dividend with respect to the WNR Common Stock to be issued in the Merger, in either case in the quarter in which the Proposed Transaction closes, which Akin Gump subsequently provided to the NTI GP Conflicts Committee and Evercore.

On December 18, 2015, NTI management had a call with Akin Gump during which NTI management provided comments to and answered questions about the terms of the proposed merger agreement. Also on December 18, 2015, Akin Gump and Vinson & Elkins discussed the Merger Agreement terms governing the rights of the NTI Unaffiliated Unitholders to receive either a pro rata cash distribution from NTI or a WNR dividend with respect to the WNR Common Stock to be issued in the Merger, in either case in the quarter in which the Proposed Transaction closes, and factors impacting the timing for the determination of, and the calculation period for, an NTI pro rata distribution. On the evening of December 18, 2015, Akin Gump provided Vinson & Elkins with a revised draft of the Merger Agreement.

On the evening of December 19, 2015, Vinson & Elkins provided Akin Gump with a revised draft of the Merger Agreement.

On December 20, 2015 and December 21, 2015, representatives of Akin Gump and Vinson & Elkins discussed the final negotiated changes to the Merger Agreement.

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On December 21, 2015, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Evercore, Akin Gump and Morris Nichols in attendance. Morris Nichols provided a summary overview of the duties of the committee in connection with its review and consideration of the Proposed Transaction. Evercore then presented its financial analysis of the proposed merger consideration contemplated by the Merger Agreement, noting that its materials and financial analyses were substantially equivalent to those most recently presented to the NTI GP Conflicts Committee, and had been updated for developments since the prior materials. After the NTI GP Conflicts Committee discussed Evercore’s presentation, representatives from Evercore confirmed that Evercore was prepared to deliver a fairness opinion to the NTI GP Conflicts Committee based on the Merger Consideration if so requested by the committee. Representatives of Akin Gump then provided an overview of the terms of the final draft of the Merger Agreement, explained the final negotiated changes to the agreement, and answered questions from the committee regarding the terms of the agreement. At the request of the NTI GP Conflicts Committee, Evercore then delivered its oral opinion, which was later confirmed by delivery of a written opinion dated December 21, 2015, that, as of December 21, 2015 and based upon and subject to the factors, procedures, assumptions, qualifications and limitations set forth therein, the Merger Consideration to be received in the Merger was fair, from a financial point of view, to the NTI Unaffiliated Unitholders. After further discussions and based on prior conclusions of the NTI GP Conflicts Committee with respect to the risks and merits of the Proposed Transaction, the NTI GP Conflicts Committee unanimously: (i) determined that the Merger Agreement and the Merger Transactions were fair and reasonable to the NTI Unaffiliated Unitholders and NTI and were not adverse to the interests of the NTI Unaffiliated Unitholders or the interests of NTI; (ii) approved the Merger Agreement and the Merger Transactions, which approval was intended to constitute “special approval” under NTI’s partnership agreement; (iii) approved the execution, delivery and performance of the Merger Agreement by NTI GP and NTI, which approvals were intended to constitute “special approval” under NTI’s partnership agreement; and (iv) recommended that the holders of NTI Common Units vote in favor of and approve the Merger Agreement and the Merger Transactions.

Later on December 21, 2015, the WNR Board held a meeting where WNR management presented materials summarizing the key terms of the Merger Agreement, which had been prepared with the assistance of Vinson & Elkins, and financial analyses based on the final negotiated Merger Consideration, which had been prepared with the assistance of Goldman Sachs. During the meeting, the WNR Board approved the Merger Transactions and Merger Agreement. Later that day, WNR and NTI management executed the definitive Merger Agreement, and following the close of trading on the NYSE, the parties issued a joint press release announcing the Merger Agreement and each of WNR and NTI filed a current report on Form 8-K with the SEC.

Following the public announcement of the Merger Agreement and the subsequent circulation of a draft of this proxy statement/prospectus, Evercore determined that certain calculations in the financial analysis it had presented to the NTI GP Conflicts Committee on December 21, 2015 needed to be revised to properly reflect the number of fully diluted shares of WNR Common Stock estimated to be outstanding following the closing of the Merger pro forma as if the Merger had closed on January 1, 2016, and the estimated amount of cash projected to be on WNR’s balance sheet following the closing of the Merger pro forma as if the Merger had closed on January 1, 2016. The revisions resulted in a reduction to the implied ranges of total value to be received by the NTI Public Unitholders in the Merger for each NTI Common Unit by approximately 4% under Evercore’s discounted cash flow analysis, precedent M&A transactions analysis, and peer group trading analysis using either the WNR Pro Forma Financial Projections—Management Pricing (as defined under “—Opinion of Evercore Group L.L.C.”) or the WNR Pro Forma Financial Projections—Historical Pricing (as defined under “—Opinion of Evercore Group L.L.C.”). Immediately following its determination, Evercore contacted the Chairman of the NTI GP Conflicts Committee and Akin Gump to inform them that Evercore had made such determination and that it would circulate a revised version of its analysis to the NTI GP Conflicts Committee and would explain the revisions.

On the morning of January 7, 2016, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Evercore, Akin Gump and Morris Nichols. At the meeting, Evercore reviewed the revisions to its financial analysis with the committee and explained that the revisions to the individual valuation ranges did

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not result in a change to the summary valuation of the Merger Consideration range of $29.00 to $32.00 per NTI Common Unit. Evercore explained that it did not consider the revisions to its analysis to be material, and that using the revised financial analysis would not have changed Evercore’s opinion that the Merger Consideration to be received in the Merger was fair, from a financial point of view, to the NTI Unaffiliated Unitholders delivered to the NTI GP Conflicts Committee on December 21, 2015. During the course of the discussions, the NTI GP Conflicts Committee asked, and representatives of Evercore answered, questions with respect to the revised financial analysis. The summary of Evercore’s opinion set forth under “—Opinion of Evercore Group L.L.C.” gives effect to the revisions. For additional information, please see “—Opinion of Evercore Group L.L.C.”

On the afternoon of January 11, 2016, the NTI GP Conflicts Committee held a telephonic meeting with representatives of Akin Gump and Morris Nichols. At the meeting, the members of the NTI GP Conflicts Committee discussed (i) the revisions to Evercore’s financial analysis as explained by Evercore at the telephonic meeting held on January 7, 2016; (ii) whether the committee required any additional information regarding the revisions and the related impact on Evercore’s financial analysis; and (iii) the implications of the revisions to the committee’s assessment of the Merger Agreement and the Merger Transactions, noting that the revisions did not affect the fairness opinion delivered to the committee by Evercore on December 21, 2015. During the course of the discussions, (i) representatives of Akin Gump and Morris Nichols responded to various questions from the committee; (ii) the committee considered various factors it had previously considered in connection with its approval of the Merger Agreement and the Merger Transactions on December 21, 2015; and (iii) the committee determined that it did not require any additional information regarding the revisions to Evercore’s financial analysis. Following the discussions, the NTI GP Conflicts Committee unanimously determined that the revisions to Evercore’s financial analysis did not change the committee’s assessment of the Merger Agreement and the Merger Transactions, and that the committee continued to recommend that NTI Common Unitholders vote in favor of the Merger Proposal.

Relationship of the Parties to the Merger

WNR owns all of the membership interests in NT InterHoldCo, which owns all of the membership interests in NTI GP and approximately 38.4% of the NTI Common Units outstanding. NT InterHoldCo has the right to appoint and remove all of the members of the NTI GP Board. Thus, through its ownership in NT InterHoldCo, WNR has a controlling interest in NTI GP, which manages the operations and activities of NTI. NTI’s assets, liabilities and results of operations are consolidated in WNR’s financial statements. During 2014, NTI’s contribution to Adjusted EBITDA represented 32.2% of WNR’s consolidated adjusted EBITDA.

The NTI GP Board includes four non-employee directors who are also directors and/or executive officers of WNR (Messrs. Foster, Stevens, Weaver and Barfield). None of Messrs. Foster, Stevens, Weaver and Barfield, however, are on the NTI GP Conflicts Committee. Persons who are directors or officers of both WNR and NTI GP owe duties to both the stockholders of WNR and to the NTI Common Unitholders and may have interests in the Merger that are different than yours. The following chart sets forth certain information, as of the date of this proxy statement/prospectus, regarding the directors and executive officers of each of WNR and NTI GP.

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WNR and NTI have also entered into certain related party transactions, including a shared services agreement, whereby NTI receives administrative support services. Under the shared services agreement, NTI also performs certain services for WNR, including risk management, legal and other related services, and receives certain services from WNRL. The shared services agreement was effective as of September 1, 2014, and was approved by the NTI GP Conflicts Committee. These services include assistance with treasury, risk management and commercial operations, environmental compliance, information technology support, legal and other related services. NTI and WNR have also engaged in several types of transactions, including the purchase and sale of crude oil, feedstocks and asphalt and the lease of railcars in the ordinary course of business. For the year ended December 31, 2014, NTI recognized $1.1 million in expense for these services, which are included in selling, general and administrative expenses in NTI’s financial statements. As of September 30, 2015, WNR owed NTI $2.2 million and NTI owed WNR $2.2 million. The full text of the shared services agreement has been filed by NTI with the SEC as Exhibit 10.2 to NTI’s Quarterly Report on Form 10-Q, filed on November 4, 2014 and is available for review without charge on the SEC’s website at www.sec.gov.

For more information on such transactions, please read the documents referenced under “Where You Can Find More Information” beginning on page 181 of this proxy statement/prospectus.

Recommendation of the NTI GP Conflicts Committee and Its Reasons for Recommending Approval of the Merger Proposal and the NTI Compensation Proposal

On December 21, 2015, the NTI GP Conflicts Committee unanimously determined that the Merger Agreement and the Merger Transactions are fair and reasonable to the NTI Unaffiliated Unitholders and NTI and are not adverse to the interests of the NTI Unaffiliated Unitholders or the interests of NTI. Based upon such determination, the NTI GP Conflicts Committee approved the Merger Agreement and the Merger Transactions, the execution, delivery and performance of the Merger Agreement by NTI GP and NTI, and the submission of the Merger Agreement and the Merger Transactions to a vote of the NTI Common Unitholders. The NTI GP Conflicts Committee’s approval constitutes “Special Approval,” as such term is defined by the NTI Partnership Agreement. The NTI GP Conflicts Committee recommends that NTI Common Unitholders vote in favor of the Merger Proposal and the NTI Compensation Proposal.

Under the NTI Partnership Agreement, whenever NTI GP, the NTI GP Board or any committee of the NTI GP Board (including the NTI GP Conflicts Committee) makes a determination or takes or declines to take any

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other action, then NTI GP, the NTI GP Board or any committee of the NTI GP Board (including the NTI GP Conflicts Committee) must make such determination or take or decline to take such other action in good faith and is not subject to any other or different standard under the NTI Partnership Agreement or applicable law (other than the implied contractual covenant of good faith and fair dealing). Under the NTI Partnership Agreement, a determination, other action or failure to act by the NTI GP Conflicts Committee will be deemed to be in “good faith” unless the NTI GP Conflicts Committee believed that such determination, other action or failure to act was adverse to the interests of the Partnership. The NTI GP Conflicts Committee has not, including, without limitation, in connection with making the determination and approvals, and the related recommendation to the NTI Common Unitholders described above, assumed any obligation to NTI or its limited partners (whether fiduciary, contractual, implied, or otherwise) other than those obligations that may exist in the NTI Partnership Agreement. Nothing in this proxy statement/prospectus or the actions, determinations or recommendations of the NTI GP Conflicts Committee described in this proxy statement/prospectus should be read to mean that the NTI GP Conflicts Committee assumed any obligations to NTI or its limited partners (whether fiduciary, contractual, implied, or otherwise) other than those obligations that may exist in the NTI Partnership Agreement. You are urged to read the full text of the NTI Partnership Agreement, which is incorporated by reference into this proxy statement/prospectus. See “Where You Can Find More Information” beginning on page 181.

The NTI GP Conflicts Committee consulted with its financial and legal advisors and considered many factors in making its determination and approvals, and the related recommendation to the NTI Common Unitholders. The NTI GP Conflicts Committee considered the following factors to be generally positive or favorable in making its determination and approvals, and the related recommendation to the NTI Common Unitholders:

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In addition, the NTI GP Conflicts Committee also considered a number of factors relating to the procedural safeguards involved in the negotiation of the Merger Agreement, including those discussed below, each of which supported its determination with respect to the fairness of the Merger to the NTI Unaffiliated Unitholders:

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The NTI GP Conflicts Committee considered the following factors to be generally negative or unfavorable in making its determination and approvals, and the related recommendation to the NTI Common Unitholders:

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The foregoing discussion of the information and factors considered by the NTI GP Conflicts Committee is not intended to be exhaustive, but includes material factors the committee considered. In view of the variety of factors considered in connection with its evaluation of the Merger and the complexity of these matters, the NTI GP Conflicts Committee did not find it useful and did not attempt to quantify or assign any relative or specific weights to the various factors considered in making its determination and recommendation. In addition, each of the members of the NTI GP Conflicts Committee may have given differing weights to different factors. Overall, the committee believed that the positive factors supporting the Merger outweighed the negative factors it considered.

WNR Parties’ Purpose and Reasons for the Merger

The WNR Parties’ reasons for the Merger include, but are not limited to:

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Position of the WNR Parties and NTI GP Conflicts Committee as to the Fairness of the Merger

Under the rules governing “going private” transactions, each of WNR and MergerCo, which are collectively referred to as the “WNR Parties,” NTI GP and NTI are deemed to be engaged in a “going private” transaction and are required to express their beliefs as to the fairness of the Merger to the NTI Unaffiliated Unitholders pursuant to Rule 13e-3 under the Exchange Act. The WNR Parties and the NTI GP Conflicts Committee, on behalf of NTI and NTI GP, are making the statements included in this section solely for the purposes of complying with the requirements of Rule 13e-3 and related rules under the Exchange Act. Although the NTI GP Conflicts Committee recommends that the NTI Common Unitholders vote to approve the Merger Agreement, the views of the WNR Parties as to the fairness of the Merger should not be construed as a recommendation to any NTI Common Unitholder as to how that unitholder should vote on the proposal to approve the Merger Agreement.

Neither the WNR Parties nor any of the directors or executive officers of NTI, other than the NTI GP Conflicts Committee, undertook any independent evaluation of the fairness of the Merger to the NTI Unaffiliated Unitholders or engaged a financial advisor for such purpose. While the vote of a majority of the outstanding NTI Common Units, including those owned by WNR and its subsidiaries, is required to approve the Merger Agreement, no separate vote of a majority of the NTI Unaffiliated Unitholders is required under the terms of the NTI Partnership Agreement. However, based on the procedural safeguards implemented during the negotiation of the Merger Agreement, which include the authorization of the NTI GP Conflicts Committee to (i) review and evaluate the terms and conditions of the proposed transaction, on behalf of NTI and the NTI Unaffiliated Unitholders, (ii) negotiate, or delegate to any person or persons the ability to negotiate, the terms and conditions of the Merger, including the consideration to be received by the NTI Unaffiliated Unitholders, (iii) determine whether or not to grant Special Approval pursuant to Section 7.9 of the NTI Partnership Agreement with respect to the Merger, (iv) make any recommendation to the NTI Unaffiliated Unitholders regarding what action, if any, should be taken by the NTI Unaffiliated Unitholders with respect to the Merger, (v) if applicable and appropriate, exercise the full authority of the NTI GP Board with respect to the approval of the Merger and the transactions contemplated thereby and (vi) retain independent professional advisors, and the other factors considered by, and the analysis, discussion and resulting conclusions of, the NTI GP Conflicts Committee described in the section entitled “—Recommendation of the NTI GP Conflicts Committee and Its Reasons for Recommending Approval of the Merger Proposal and the NTI Compensation Proposal,” which analysis, discussion and resulting conclusions the WNR Parties expressly adopt as their own, the WNR Parties believe that the Merger is substantively and procedurally fair to the NTI Unaffiliated Unitholders.

The foregoing discussion of the information and factors considered and given weight by the WNR Parties and the NTI GP Conflicts Committee, on behalf of NTI GP, is not intended to be exhaustive, but includes the factors considered by the WNR Parties and the NTI GP Conflicts Committee that each believes to be material to

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the fairness determination regarding the fairness of the Merger for the purpose of complying with the requirements of Rule 13e-3 and the related rules under the Exchange Act. The WNR Parties and the NTI GP Conflicts Committee did not find it practicable to, and did not, quantify or otherwise attach relative weights to the foregoing factors in reaching their position as to the fairness of the Merger. Rather, the WNR Parties and the NTI GP Conflicts Committee, on behalf of NTI GP, made their fairness determination after considering all of the factors as a whole.

Projected Financial Information

Set forth below is a summary of certain projected financial information, referred to as the “Management Projections,” that was prepared by WNR management and furnished to the WNR Board and the NTI GP Conflicts Committee for purposes of evaluating the proposed Merger. This projected financial information was also provided to Evercore for use in connection with its financial analyses and opinion and to Goldman Sachs for use in connection with its financial analyses. The Management Projections were prepared by WNR management utilizing standalone projected financial information for NTI based on preliminary budgeting and forecast information, as updated and refined based upon input from NTI management during the Merger process, and further adjusted, in the case of the projections related to WNR pro forma for the Merger, for WNR’s assumed future divestiture of NTI’s traditional logistics assets to WNRL. The Management Projections consist of one set of projections prepared reflecting WNR management’s crack spread assumptions (the “WNR Management Pricing Case”) and a second set, prepared at the request of the NTI GP Conflicts Committee and Evercore based on input from NTI management, based on NTI’s budget for the 2016 period and the application of five-year historical average crack spreads to the 2017 to 2020 periods (the “Historical Pricing Case”). The Management Projections are dated December 1, 2015, and were provided to the NTI GP Conflicts Committee and Evercore on December 2, 2015.

WNR and NTI do not as a matter of course make public projections as to future sales, earnings, or other results. However, WNR management has prepared the prospective financial information set forth below for the purposes of evaluating the proposed Merger. The accompanying prospective financial information was not prepared with a view toward public disclosure or with a view toward complying with the guidelines established by the American Institute of Certified Public Accountants with respect to prospective financial information, but, in the view of WNR management, was prepared on a reasonable basis, reflected the then best currently available estimates and judgments, and presents, to the best of management’s knowledge and belief, the expected course of action and the expected future financial performance of WNR, WNRL and NTI. However, this information is not fact and should not be relied upon as being necessarily indicative of future results, and readers of this proxy statement/prospectus are cautioned not to place undue reliance on the prospective financial information.

Neither our independent registered public accounting firm, nor any other independent accountants, have compiled, examined or performed any procedures with respect to the prospective financial information contained herein, nor have they expressed any opinion or any other form of assurance on such information or its achievability, and assume no responsibility for, and disclaim any association with, the prospective financial information.

WNR Management Pricing Case:

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Historical Pricing Case:

The foregoing projected financial information is based, in part, on the assumptions set forth in the table below: