<PAGE>
 
                                                                     Exhibit 4.4



================================================================================

                                CLARK USA, INC.


               11 1/2% SUBORDINATED EXCHANGE DEBENTURES DUE 2009


                     -------------------------------------


                            SUPPLEMENTAL INDENTURE

                          Dated as of August 10, 1998

                                      to

                                   INDENTURE

                          Dated as of October 1, 1997


                     -------------------------------------
                                        
                                        
                            BANKERS TRUST COMPANY,

                                    Trustee

================================================================================
<PAGE>
 
          SUPPLEMENTAL INDENTURE (this "Supplemental Indenture"), dated as of
August 10, 1998, by and between CLARK USA, INC., a Delaware corporation (the
"Company"), having its principal office at 8182 Maryland Avenue, St. Louis,
Missouri 63105-3721, and Bankers Trust Company, as trustee (the "Trustee") under
the Indenture (as defined below), having its Corporate Trust and Agency Office
at Four Albany Street, New York, New York 10006. Capitalized terms used but not
defined herein shall have the meanings assigned to such terms in the Indenture.

          WHEREAS, the Company and the Trustee previously duly executed, and the
Company duly delivered to the Trustee, an Indenture dated as of October 1, 1997
(the "Indenture"), relating to the Company's 11 1/2% Subordinated Exchange
Debentures due 2009 (the "Securities") into which the Company's 11 1/2% Senior
Cumulative Exchangeable Preferred Stock (the "Preferred Stock") is exchangeable;

          WHEREAS, pursuant to Section 8.02 of the Indenture, the Company and
the Trustee have obtained the consent of the Holders of not less than a majority
of the outstanding shares of Preferred Stock to the amendments made hereby;

          WHEREAS, the Board of Directors of the Company has authorized the
execution of this Supplemental Indenture and its delivery to the Trustee;

          WHEREAS, the Company has delivered an Opinion of Counsel to the
Trustee pursuant to Sections 1.02 and 8.03 of the Indenture; and

          WHEREAS, all other actions necessary to make this Supplemental
Indenture a legal, valid and binding obligation of the parties hereto in
accordance with its terms and the terms of the Indenture have been performed;

          NOW, THEREFORE, in consideration of the promises contained herein and
for other good and valuable consideration, the receipt and sufficiency of which
is hereby acknowledged, the Company and the Trustee hereby mutually covenant and
agree for the equal and proportionate benefit of all Holders of the Securities
as follows:

                                   ARTICLE I
                                  AMENDMENTS

          Upon execution of this Supplemental Indenture, the terms of the
Securities and the Indenture shall be amended as follows:

          SECTION I.1.  Section 1.01 of the Indenture shall be amended as
follows:

          (a)  by deleting the definition of "Permitted Indebtedness" and
substituting in lieu thereof the following:

          "'Permitted Indebtedness' means Indebtedness incurred by the
     Corporation or its Restricted Subsidiaries (i) to renew, extend, refinance
     or refund Indebtedness that is permitted to be incurred pursuant to clauses
     (ii) through (iv) and clause (xi) below; provided, however, that such
     Indebtedness does not exceed the principal amount of the Indebtedness so
     renewed, extended, refinanced or refunded plus the amount of any premium
     required to be paid in connection with such refinancing pursuant to the
     terms of the Indebtedness refinanced or the amount of any premium
     reasonably determined by the Corporation or such Restricted Subsidiary as
     necessary to accomplish such refinancing by means of a tender offer or
     privately negotiated repurchase, plus the expenses of the Corporation or
     such Restricted Subsidiary incurred in connection with such refinancing;
     and provided, however, that Indebtedness the proceeds of which are used to
     refinance or refund such Indebtedness shall only be permitted if (A) in the
     case of any refinancing or refunding of Indebtedness that is pari passu
     with the Exchange Debentures the Refinancing or refunding Indebtedness is
     made pari passu with the Exchange Debentures or subordinated to the
     Exchange Debentures, (B) in the case of any refinancing or refunding of
     Indebtedness that is subordinated to the Exchange Debentures the
     refinancing or refunding of Indebtedness is made subordinated to the
     Exchange Debentures at least to the same extent as such Indebtedness being
     refinanced or refunded was subordinated to the Exchange Debentures and (C)
     in the case of the refinancing or refunding of

<PAGE>
 
     Indebtedness that is subordinated to the Exchange Debentures, the
     refinancing or refunding Indebtedness by its terms, or by the terms of any
     agreement or instrument pursuant to which such Indebtedness is issued, (x)
     does not provide for payments of principal of such Indebtedness at the
     stated maturity thereof or by way of a sinking fund applicable thereto or
     by way of any mandatory redemption, defeasance, retirement or repurchase
     thereof by the Corporation or such Restricted Subsidiary (including any
     redemption, retirement or repurchase which is contingent upon events or
     circumstances, but excluding any retirement required by virtue of
     acceleration of such Indebtedness upon an event of default thereunder), in
     each case prior to the final Stated Maturity of the Exchange Debentures and
     (y) does not permit redemption or other retirement (including pursuant to
     an offer to purchase made by the Corporation or such Restricted Subsidiary)
     of such Indebtedness at the option of the holder thereof prior to the final
     stated maturity of the Indebtedness being refinanced or refunded, other
     than a redemption or other retirement at the option of the holder of such
     Indebtedness (including pursuant to an offer to purchase made by the
     Corporation or such Restricted Subsidiary), which is conditioned upon the
     change of control of the Corporation or such Restricted Subsidiary); (ii)
     arising from time to time under the Credit Agreement or any refinancings,
     renewals, extensions, refundings or replacements thereof or extensions of
     credit to finance working capital requirements in an aggregate principal
     amount not to exceed the greater of (a) $700 million at any one time
     outstanding less the aggregate amount of all proceeds of all asset
     dispositions that have been applied since the Issue Date to permanently
     reduce the outstanding amount of such Indebtedness and (b) the amount of
     the Borrowing Base on such date (calculated on a pro forma basis after
     giving effect to such borrowing and the application of the proceeds
     therefrom); (iii) outstanding on the Issue Date; (iv) evidenced by trade
     letters of credit incurred in the ordinary course of business not to exceed
     $20 million in the aggregate at any time; (v) between or among the
     Corporation and/or its Restricted Subsidiaries other than Restricted
     Subsidiaries owned in any part by the Principal Shareholders; (vi) which is
     Junior Subordinated Indebtedness; (vii) arising out of Sale and Leaseback
     Transactions or Capitalized Lease Obligations relating to computers and
     other office equipment and elements, catalysts or other chemicals used in
     connection with the refining of petroleum or petroleum by-products; (viii)
     the proceeds of which are used to make the Chevron Payment, the AOC Payment
     and the Gulf Payments; (ix) arising out of Interest Swap Obligations; (x)
     in connection with capital projects qualifying under Section 142(a) (or any
     successor provision) of the Internal Revenue Code of 1986, as amended, in
     an amount not to exceed $75 million in the aggregate at any time; (xi) to
     finance the Lima Acquisition, in an amount not to exceed $250 million; and
     (xii) in addition to Indebtedness permitted by clauses (i) through (xi)
     above, Indebtedness not to exceed on a consolidated basis for the
     Corporation and its Restricted Subsidiaries at any time $50 million."

          (b)  by adding the following definition in appropriate alphabetical
order:

          "'Lima Acquisition' means the acquisition by Clark Refining &
     Marketing, Inc. of the Lima Oil Refinery located in Lima, Ohio, and certain
     related inventory, spare parts and other assets, pursuant to the Agreement
     for the Purchase and Sale of Lima Oil Refinery, dated as of July 1, 1998,
     among Clark Refining & Marketing, Inc. and BP Exploration & Oil Inc., The
     Standard Oil Company, BP Oil Pipeline Company and BP Chemicals Inc."


                                  ARTICLE II
                                 MISCELLANEOUS

          SECTION II.1.  For all purposes of this Supplemental Indenture, except
as otherwise herein expressly provided or unless the context otherwise requires:
(A) the terms and expressions used herein shall have the same meanings as
corresponding terms and expressions used in the Indenture and (B) the words
"herein," "hereof" and "hereby" and other words of similar import used in this
Supplemental Indenture refer to this Supplemental Indenture as a whole and not
any particular Article, Section or other subdivision.

          SECTION II.2.  Upon execution of this Supplemental Indenture, the
Indenture shall be modified in accordance herewith, but except as expressly
amended hereby, the Indenture is in all respects ratified and confirmed and all
the terms, conditions and provisions thereof shall remain in full force and
effect.

          SECTION II.3.  Upon execution, this Supplemental Indenture shall form
a part of the Indenture and the Supplemental Indenture and the Indenture shall
be read, taken and construed as one and the same instrument

<PAGE>
 
for all purposes, and every holder of Securities heretofore or hereafter
authenticated and delivered under the Indenture shall be bound hereby.

          SECTION II.4.  This Supplemental Indenture shall become effective as
of the date first above written.

          SECTION II.5.  The Trustee accepts the amendment to the Indenture
effected by this Supplemental Indenture and agrees to execute the trust created
by the Indenture, as hereby amended, but only upon the terms and conditions set
forth in the Indenture, as hereby amended, including the terms and provisions
defining and limiting the liabilities and responsibilities of the Trustee, which
terms and provisions shall in like manner define and limit the Trustee's
liabilities in the performance of the trust created by the Indenture, as hereby
amended. Without limiting the generality of the foregoing, the Trustee has no
responsibility for the correctness of the recitals of fact herein contained
which shall be taken as the statements of the Company and makes no
representations as to the validity or sufficiency of this Supplemental
Indenture, except as to the due and valid execution hereof by the Trustee, and
shall incur no liability or responsibility in respect of the validity thereof.
The Trustee's execution of this Supplemental Indenture should not be construed
to be an approval or disapproval of the advisability of the amendments to the
Indenture provided herein.

          SECTION II.6.  THIS SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY, AND
CONSTRUED IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK APPLICABLE TO
AGREEMENTS MADE AND TO BE PERFORMED ENTIRELY IN SAID STATE.

          SECTION II.7.  This Supplemental Indenture may be executed in any
number of counterparts, each of which when so executed shall be deemed to be an
original, and all of such counterparts shall together constitute one and the
same instrument.

          IN WITNESS WHEREOF, the parties hereto have caused this Supplemental
Indenture to be duly executed as of the day and year first above written.


                           CLARK USA, INC.


                           By:  Maura J. Clark
                                ------------------------------------------------
                                Name:  Maura J. Clark
                                Title: Executive Vice President-Corporate
                                         Development and Chief Financial Officer


                           BANKERS TRUST COMPANY, as Trustee


                           By:  Susan Johnson
                                ------------------------------------------------
                                Name:  Susan Johnson
                                Title: Assistant Vice President