Document:

exv4w6

 

EXHIBIT
4.6

Second Amended and Restated

Bylaws

of

US BioEnergy Corporation

a South Dakota Corporation

 

 

TABLE OF CONTENTS

	 	 	 	 	 
	 	 	Page	 
	ARTICLE I OFFICES
	 	 	1	 
	Section 1. Registered Office
	 	 	1	 
	Section 2. Other Offices
	 	 	1	 
	ARTICLE II MEETINGS OF SHAREHOLDERS
	 	 	1	 
	Section 1. Place of Meetings
	 	 	1	 
	Section 2. Annual Meetings
	 	 	1	 
	Section 3. Special Meetings
	 	 	1	 
	Section 4. Nature of Business at Meetings of Shareholders
	 	 	2	 
	Section 5. Nomination of Directors
	 	 	4	 
	Section 6. Notice; Waiver
	 	 	6	 
	Section 7. Adjournments
	 	 	7	 
	Section 8. Quorum
	 	 	7	 
	Section 9. Voting
	 	 	7	 
	Section 10. Proxies
	 	 	8	 
	Section 11. List of Shareholders Entitled to Vote
	 	 	8	 
	Section 12. Record Date
	 	 	9	 
	Section 13. Stock Ledger
	 	 	9	 
	Section 14. Conduct of Meetings
	 	 	9	 
	Section 15. Inspectors of Election
	 	 	10	 
	Section 16. Cumulative Voting
	 	 	11	 
	ARTICLE III DIRECTORS
	 	 	11	 
	Section 1. Number and Election of Directors
	 	 	11	 
	Section 2. Vacancies
	 	 	12	 
	Section 3. Duties and Powers
	 	 	12	 
	Section 4. Meetings; Waiver of Notice
	 	 	13	 
	Section 5. Organization
	 	 	13	 
	Section 6. Resignations and Removals of Directors
	 	 	13	 
	Section 7. Quorum
	 	 	14	 
	Section 8. Actions of the Board by Written Consent
	 	 	14	 
	Section 9. Meetings by Means of Conference Telephone
	 	 	15	 
	Section 10. Committees
	 	 	15	 
	Section 11. Compensation
	 	 	16	 
	Section 12. Directors’ Assent
	 	 	16	 
	ARTICLE IV OFFICERS
	 	 	16	 
	Section 1. General
	 	 	16	 
	Section 2. Election
	 	 	17	 
	Section 3. Voting Securities Owned by the Corporation
	 	 	17	 
	Section 4. Chairman of the Board of Directors
	 	 	18	 

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	 	 	Page	 
	Section 5. Chief Executive Officer
	 	 	18	 
	Section 6. President
	 	 	18	 
	Section 7. Chief Financial Officer
	 	 	19	 
	Section 8. Vice Presidents
	 	 	19	 
	Section 9. Corporate Secretary
	 	 	20	 
	Section 10. Treasurer
	 	 	20	 
	Section 11. Assistant Corporate Secretaries
	 	 	21	 
	Section 12. Assistant Treasurers
	 	 	21	 
	Section 13. Other Officers
	 	 	22	 
	ARTICLE V STOCK
	 	 	22	 
	Section 1. Form of Certificates
	 	 	22	 
	Section 2. Signatures
	 	 	23	 
	Section 3. Lost Certificates
	 	 	23	 
	Section 4. Transfers
	 	 	23	 
	Section 5. Dividend Record Date
	 	 	24	 
	Section 6. Record Owners
	 	 	24	 
	Section 7. Transfer and Registry Agents
	 	 	24	 
	ARTICLE VI GENERAL PROVISIONS
	 	 	25	 
	Section 1. Dividends
	 	 	25	 
	Section 2. Disbursements
	 	 	25	 
	Section 3. Fiscal Year
	 	 	25	 
	ARTICLE VII INDEMNIFICATION
	 	 	25	 
	Section 1. Director and Officer Indemnification; Advancement of Expenses
	 	 	25	 
	Section 2. Survival of Indemnification and Advancement of Expenses
	 	 	26	 
	Section 3. Non-Exclusiveness
	 	 	26	 
	Section 4. Purchase of Insurance
	 	 	26	 
	Section 5. Indemnification of Employees and Agents
	 	 	27	 
	ARTICLE VIII AMENDMENTS
	 	 	27	 
	Section 1. Amendments
	 	 	27	 
	Section 2. Entire Board of Directors
	 	 	27	 

 

 

Bylaws

of

US BioEnergy Corporation

(hereinafter called the “Corporation”)

ARTICLE I

OFFICES

     Section 1. Registered Office. The registered office of the Corporation shall be fixed
in the Corporation’s articles of incorporation, as the same may be amended from time to time.

     Section 2. Other Offices. The Corporation may also have offices at such other places,
both within and without the State of South Dakota, as the Board of Directors may determine from
time to time.

ARTICLE II

MEETINGS OF SHAREHOLDERS

     Section 1. Place of Meetings. Meetings of the shareholders for the election of
directors or for any other purpose shall be held at such time and place, either within or without
the State of South Dakota, as shall be designated from time to time by the Board of Directors.

     Section 2. Annual Meetings. The Annual Meeting of Shareholders for the election of
directors shall be held on such date and at such time and place as shall be designated from time to
time by the Board of Directors. Any other proper business may be transacted at the Annual Meeting
of Shareholders.

     Section 3. Special Meetings. Special meetings of the shareholders, for any purpose or purposes, unless otherwise
prescribed by statute, may be called by (i) the Chairman of

 

 

the Board of Directors, (ii) the Board
of Directors or (iii) written demand, signed, dated and delivered to the Corporation by the holders
of not less than twenty-five percent (25%) of all the outstanding shares of the Corporation
entitled to vote at the meeting, describing the purpose or purposes for which the meeting is to be
held. At a Special Meeting of Shareholders, only such business within the purposes described in
the notice of meeting (or any supplement thereto) shall be conducted.

     Section 4. Nature of Business at Meetings of Shareholders. No business may be
transacted at an Annual Meeting of Shareholders, other than business that is either (a) specified
in the notice of meeting (or any supplement thereto) given by or at the direction of the Board of
Directors (or any duly authorized committee thereof), (b) otherwise properly brought before the
Annual Meeting by or at the direction of the Board of Directors (or any duly authorized committee
thereof), or (c) otherwise properly brought before the Annual Meeting by any shareholder of the
Corporation (i) who is a shareholder of record on the date of the giving of the notice provided for
in this Section 4 and on the record date for the determination of shareholders entitled to notice
of and to vote at such Annual Meeting and (ii) who complies with the notice procedures set forth in
this Section 4.

     In addition to any other applicable requirements, for business to be properly brought before
an Annual Meeting by a shareholder, such shareholder must have given timely notice thereof in
proper written form to the Corporate Secretary.

     To be timely, a shareholder’s notice to the Corporate Secretary must be delivered to or mailed
and received at the principal executive offices of the Corporation not less than ninety (90) days
nor more than one hundred twenty (120) days prior to the anniversary date of
the immediately preceding Annual Meeting of Shareholders; provided, however,
that in the event

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that the Annual Meeting is called for a date that is not within thirty (30) days
before or after such anniversary date, notice by the shareholder in order to be timely must be so
received not later than the close of business on the tenth (10th) day following the day on which
such notice of the date of the Annual Meeting was mailed or such public disclosure of the date of
the Annual Meeting was made, whichever first occurs.

     To be in proper written form, a shareholder’s notice to the Corporate Secretary must set forth
as to each matter such shareholder proposes to bring before the Annual Meeting (i) a brief
description of the business desired to be brought before the Annual Meeting and the reasons for
conducting such business at the Annual Meeting, (ii) the name and record address of such
shareholder, (iii) the class or series and number of shares of capital stock of the Corporation
which are owned beneficially or of record by such shareholder, (iv) a description of all
arrangements or understandings between such shareholder and any other person or persons (including
their names) in connection with the proposal of such business by such shareholder and any material
interest of such shareholder in such business and (v) a representation that such shareholder
intends to appear in person or by proxy at the Annual Meeting to bring such business before the
meeting.

     No business shall be conducted at the Annual Meeting of Shareholders except business brought
before the Annual Meeting in accordance with the procedures set forth in this Section 4;
provided, however, that, once business has been properly brought before the Annual
Meeting in accordance with such procedures, nothing in this Section 4 shall be deemed to preclude
discussion by any shareholder of any such business. If the chairman of an Annual Meeting
determines that business was not properly brought before the Annual Meeting in
accordance with the foregoing procedures, the chairman shall declare to the meeting that the

3

 

business was not properly brought before the meeting and such business shall not be transacted. No
business shall be conducted at a Special Meeting of Shareholders except for such business as shall
have been brought before the meeting pursuant to the Corporation’s notice of meeting.

     Section 5. Nomination of Directors. Only persons who are nominated in accordance with
the following procedures shall be eligible for election as directors of the Corporation, except as
may be otherwise provided in the Articles of Incorporation with respect to the right of holders of
preferred stock of the Corporation to nominate and elect a specified number of directors in certain
circumstances. Nominations of persons for election to the Board of Directors may be made at any
Annual Meeting of Shareholders, or at any Special Meeting of Shareholders called for the purpose of
electing directors, (a) by or at the direction of the Board of Directors (or any duly authorized
committee thereof) or (b) by any shareholder of the Corporation (i) who is a shareholder of record
on the date of the giving of the notice provided for in this Section 5 and on the record date for
the determination of shareholders entitled to vote at such meeting and (ii) who complies with the
notice procedures set forth in this Section 5.

     In addition to any other applicable requirements, for a nomination to be made by a
shareholder, such shareholder must have given timely notice thereof in proper written form to the
Corporate Secretary.

     To be timely, a shareholder’s notice to the Corporate Secretary must be delivered to or mailed
and received at the principal executive offices of the Corporation (a) in the case of an Annual
Meeting, not less than ninety (90) days nor more than one hundred twenty (120) days prior to the
anniversary date of the immediately preceding Annual Meeting of Shareholders;
provided, however, that in the event that the Annual Meeting is called for a
date that is not within thirty (30) days before or after such anniversary date, notice by the
shareholder in order to be

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timely must be so received not later than the close of business on the
tenth (10th) day following the day on which such notice of the date of the Annual Meeting was
mailed or such public disclosure of the date of the Annual Meeting was made, whichever first
occurs; and (b) in the case of a Special Meeting of Shareholders called for the purpose of electing
directors, not later than the close of business on the tenth (10th) day following the day on which
notice of the date of the Special Meeting was mailed or public disclosure of the date of the
Special Meeting was made, whichever first occurs.

     To be in proper written form, a shareholder’s notice to the Corporate Secretary must set forth
(a) as to each person whom the shareholder proposes to nominate for election as a director (i) the
name, age, business address and residence address of the person, (ii) the principal occupation or
employment of the person, (iii) the class or series and number of shares of capital stock of the
Corporation which are owned beneficially or of record by the person and (iv) any other information
relating to the person that would be required to be disclosed in a proxy statement or other filings
required to be made in connection with solicitations of proxies for election of directors pursuant
to Section 14 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and the
rules and regulations promulgated thereunder; and (b) as to the shareholder giving the notice (i)
the name and record address of such shareholder, (ii) the class or series and number of shares of
capital stock of the Corporation which are owned beneficially or of record by such shareholder,
(iii) a description of all arrangements or understandings between such shareholder and each
proposed nominee and any other person or persons (including their names) pursuant to which the
nomination(s) are to be made by such shareholder,
(iv) a representation that such shareholder intends to appear in person or by proxy at the
meeting to nominate the persons named in its notice and (v) any other information relating to such

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shareholder that would be required to be disclosed in a proxy statement or other filings required
to be made in connection with solicitations of proxies for election of directors pursuant to
Section 14 of the Exchange Act and the rules and regulations promulgated thereunder. Such notice
must be accompanied by a written consent of each proposed nominee to being named as a nominee and
to serve as a director if elected.

     No person shall be eligible for election as a director of the Corporation unless nominated in
accordance with the procedures set forth in this Section 5. If the chairman of the meeting
determines that a nomination was not made in accordance with the foregoing procedures, the chairman
shall declare to the meeting that the nomination was defective and such defective nomination shall
be disregarded.

     Section 6. Notice; Waiver. Except for the increase of stock and indebtedness of the
Corporation when sixty (60) days’ notice is required by Article XVII, Section 8, of the
Constitution of the State of South Dakota, whenever shareholders are required or permitted to take
any action at a meeting, a written notice of the meeting shall be given which shall state the date,
time and place of the meeting and, in the case of a Special Meeting, the purpose or purposes for
which the meeting is called. Unless otherwise required by law, written notice of any meeting shall
be given not less than ten (10) nor more than sixty (60) days before the date of the meeting to
each shareholder entitled to notice of and to vote at such meeting. A shareholder may waive any
notice required by applicable law, the Articles of Incorporation, or these Bylaws, before or after
the date and time stated in the notice. The waiver shall be in writing, signed by the shareholder
entitled to the
notice, and shall be delivered to the Corporation for inclusion in the minutes or filing with
the corporate records.

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     Section 7. Adjournments. Any meeting of the shareholders may be adjourned from time
to time to reconvene at the same or some other place, and notice need not be given of any such
adjourned meeting if the date, time and place thereof are announced at the meeting before
adjournment. At the adjourned meeting, the Corporation may transact any business which might have
been transacted at the original meeting. If the adjournment is for more than one hundred twenty
(120) days, or if after the adjournment a new record date is fixed for the adjourned meeting,
notice of the adjourned meeting in accordance with the requirements of Section 6 hereof shall be
given to each shareholder of record entitled to notice of and to vote at the meeting.

     Section 8. Quorum. Unless otherwise required by applicable law or the Articles of
Incorporation, a majority of the votes entitled to be cast on a matter constitutes a quorum for
action on that matter. A quorum, once established, shall not be broken by the withdrawal of enough
votes to leave less than a quorum. If, however, such quorum shall not be present or represented at
any meeting of the shareholders, the shareholders entitled to vote thereat, present in person or
represented by proxy, shall have power to adjourn the meeting from time to time, in the manner
provided in Section 7 hereof, until a quorum shall be present or represented.

     Section 9. Voting. Unless otherwise required by law, the Articles of Incorporation or
these Bylaws, any action brought before any meeting of the shareholders, other than the election of
directors, shall be approved if the votes cast favoring such action exceed the votes cast opposing
such action. Unless otherwise provided in the Articles of Incorporation, and subject to Section 12
of this Article II, each shareholder represented at a meeting of the shareholders shall be entitled
to cast one (1) vote for each share of the capital stock entitled to

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vote thereat held by such
shareholder. Such votes may be cast in person or by proxy as provided in Section 10 of this
Article II. The Board of Directors, in its discretion, or the officer of the Corporation presiding
at a meeting of the shareholders, in such officer’s discretion, may require that any votes cast at
such meeting shall be cast by written ballot.

     Section 10. Proxies. At each meeting of the Corporation’s shareholders, a shareholder
or the shareholder’s agent or attorney-in-fact may appoint a proxy to vote or otherwise act for the
shareholder by singing an appointment form, or by an electronic transmission. An electronic
transmission shall contain or shall be accompanied by information from which one can determine that
the shareholder or the shareholder’s agent or attorney-in-fact authorized the transmission. An
appointment of a proxy is effective when a signed appointment form or an electronic transmission of
the appointment is received by the inspector of election or the Corporate Secretary. An
appointment is valid for eleven (11) months unless a longer period is expressly provided in the
appointment form.

     Section 11. List of Shareholders Entitled to Vote. After fixing a record date for a
meeting, the officer of the Corporation who has charge of the stock transfer books for shares of
the Corporation shall make a complete list of the shareholders entitled to vote at any meeting of
shareholders, or any adjournment thereof, arranged in alphabetical order by voting group, and
within each voting group by class or series of shares, showing the address of and the number of
shares held by each shareholder. Such list
shall be available for inspection by any shareholder, beginning two (2) business days after
notice of the meeting of shareholders is given for which the list was prepared and continuing
through the meeting, at the Corporation’s principal office or at a place identified in the meeting
notice in the city where the meeting will be held. The Corporation shall make the shareholders’
list available at the meeting, and any

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shareholder, shareholder’s agent or attorney shall be
entitled to inspect the list at any time during the meeting or any adjournment thereof. The
original stock transfer books shall be prima facie evidence as to whom are the shareholders
entitled to examine such list or transfer books or to vote at any meeting of shareholders. Failure
to comply with the requirements of this section shall not affect the validity of any action taken
at such meeting.

     Section 12. Record Date. In order to determine the shareholders entitled to notice of
a shareholders’ meeting, to demand a special meeting, to vote or to take any other action, the
Board of Directors may fix a future date as the record date, which record date shall not be more
than seventy (70) days before the meeting or action requiring a determination of shareholders. If
no record date is fixed by the Board of Directors, the record date for determining shareholders
entitled to notice of or to vote at a meeting of the shareholders shall be at the close of business
on the day next preceding the day on which notice is given. A determination of shareholders
entitled to notice of or to vote at a shareholder’s meeting is effective for any adjournment of the
meeting unless the Board of Directors fixes a new record date, which it must do if the meeting is
adjourned to a date more than one hundred twenty (120) days after the date fixed for the original
meeting.

     Section 13. Stock Ledger. The stock ledger of the Corporation shall be the only
evidence as to who are the shareholders entitled to examine the stock ledger, the list required by
Section 11 of this Article II
or the books of the Corporation, or to vote in person or by proxy at any meeting of the
shareholders.

     Section 14. Conduct of Meetings. The Board of Directors of the Corporation may adopt
by resolution such rules and regulations for the conduct of any meeting of the shareholders as it
shall deem appropriate. Except to the extent inconsistent with such rules and

9

 

regulations as
adopted by the Board of Directors, the chairman of any meeting of the shareholders shall determine
the order of business and may establish rules for the conduct of the meeting. Such rules,
regulations or procedures, whether adopted by the Board of Directors or prescribed by the chairman
of the meeting, may include, without limitation, the following: (i) the establishment of an agenda
or order of business for the meeting; (ii) the determination of when the polls shall open and close
for any given matter to be voted on at the meeting; (iii) rules and procedures for maintaining
order at the meeting and the safety of those present; (iv) limitations on attendance at or
participation in the meeting to shareholders of record of the Corporation, their duly authorized
and constituted proxies or such other persons as the chairman of the meeting shall determine; (v)
restrictions on entry to the meeting after the time fixed for the commencement thereof; and (vi)
limitations on the time allotted to questions or comments by participants.

     Section 15. Inspectors of Election. In advance of any meeting of the shareholders,
the Board of Directors by resolution, the Chairman if there be one, or the Chief Executive Officer,
shall appoint one or more inspectors to act at the meeting and make a written report of the
inspector’s determinations. One or more other persons may be designated as alternate inspectors to
replace any inspector who fails to act. If no inspector or alternate is able to act at a meeting
of the shareholders, the
chairman of the meeting shall appoint one or more inspectors to act at the meeting. Unless
otherwise required by applicable law, inspectors may be officers or employees of the Corporation.
Each inspector shall take and sign an oath faithfully to execute the duties of inspector with
strict impartiality and according to the best of such inspector’s ability. The inspector shall
have the duties prescribed by law and shall take charge of

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the polls and, when the vote is
completed, shall make a certificate of the result of the vote taken and of such other facts as may
be required by applicable law.

     Section 16. Cumulative Voting. At each election of directors every shareholder
entitled to vote at such election shall have the right to vote, in person or by proxy, the number
of shares owned by such shareholder for as many persons as there are directors to be elected and
for whose election such shareholder has a right to vote, or to cumulate such shareholder’s votes by
multiplying the number of votes that such shareholder is entitled to cast by the number of
directors for whom such shareholder is entitled to vote and casting the product for a single
candidate or distributing the product among two or more candidates.

ARTICLE III

DIRECTORS

     Section 1. Number and Election of Directors. The number of directors shall be fixed
as provided in the Articles of Incorporation. The directors shall be divided into three classes,
designated Class I, Class II and Class III. Each class shall consist, as nearly as may be
possible, of one-third of the total number of directors constituting the entire Board of Directors.
The initial division of the Board of Directors into classes shall be made by the decision of the
affirmative vote of a majority of the entire Board of Directors. The term of the initial Class I
directors shall terminate on the date of
the 2007 Annual Meeting; the term of the initial Class II directors shall terminate on the
date of the 2008 Annual Meeting; and the term of the initial Class III directors shall terminate on
the date of the 2009 Annual Meeting or, in each case, upon such director’s earlier death,
resignation or removal. At each succeeding Annual Meeting of Shareholders beginning in 2007,
successors to the class of directors whose term expires at that Annual Meeting shall be elected for
a three (3) year term and until their successors are duly elected and qualified. If the number of
directors is changed, any increase or decrease shall be

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apportioned among the classes so as to
maintain the number of directors in each class as nearly equal as possible, and any additional
director of any class elected to fill a vacancy resulting from an increase in such class or from
the removal from office, death, disability, resignation or disqualification of a director or other
cause shall hold office for a term that shall coincide with the remaining term of that class, but
in no case will a decrease in the number of directors have the effect of removing or shortening the
term of any incumbent director. Except as provided in Section 2 of this Article III, directors
shall be elected by a plurality of the votes cast at each Annual Meeting of Shareholders and each
director so elected shall hold office until such director’s term expires and until such director’s
successor is duly elected and qualified, or until such director’s earlier death, resignation or
removal. Directors need not be shareholders.

     Section 2. Vacancies. Any vacancy on the Board of Directors that results from an
increase in the number of directors may only be filled by a majority of the Board of Directors then
in office, provided that a quorum is present, and any other vacancy occurring on the Board of
Directors may only be filled, as long as there is at least one director in office, by a majority of
the Board of Directors then in office, even if less than a quorum, or by a sole remaining director.
Any director
of any class elected to fill a vacancy resulting from an increase in the number of directors
of such class shall hold office for a term that shall coincide with the remaining term of that
class. Any director elected to fill a vacancy not resulting from an increase in the number of
directors shall have the same remaining term as that of his or her predecessor.

     Section 3. Duties and Powers. The business and affairs of the Corporation shall be
managed by or under the direction of the Board of Directors which may exercise all such powers of
the Corporation and do all such lawful acts and things as are not by statute, the Articles of
Incorporation or these Bylaws required to be exercised or done by the shareholders.

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     Section 4. Meetings; Waiver of Notice. The Board of Directors may hold meetings, both
regular and special, either within or without the State of South Dakota. Regular meetings of the
Board of Directors may be held without notice at such time and at such place as may from time to
time be determined by the Board of Directors. Special meetings of the Board of Directors may be
called by the Chairman, if there be one, or the Chief Executive Officer. Notice thereof stating
the place, date and hour of the meeting shall be given to each director either by mail not less
than forty-eight (48) hours before the date of the meeting, by telephone, telegram or electronic
means on twenty-four (24) hours’ notice, or on such shorter notice as the person or persons calling
such meeting may deem necessary or appropriate in the circumstances. A director may waive any
notice required by applicable law, the Articles of Incorporation or these Bylaws, before or after
the date and time stated in the notice. Except as provided by applicable law, the waiver shall be
in writing, signed by the director entitled to the notice and filed with the minutes or corporate
records.

     Section 5. Organization. At each meeting of the Board of Directors, the Chairman of the Board of Directors or, in
the Chairman’s absence or if there be none, a director chosen by a majority of the directors
present, shall act as chairman. The Corporate Secretary shall act as secretary at each meeting of
the Board of Directors. In case the Corporate Secretary shall be absent from any meeting of the
Board of Directors, an Assistant Corporate Secretary shall perform the duties of secretary at such
meeting; and in the absence from any such meeting of the Corporate Secretary and all the Assistant
Corporate Secretaries, the chairman of the meeting may appoint any person to act as secretary of
the meeting.

     Section 6. Resignations and Removals of Directors. Any director of the Corporation
may resign at any time, by giving notice in writing or by electronic transmission to

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the Chairman
of the Board of Directors, if there be one, the Chief Executive Officer or the Corporate Secretary.
Such resignation shall take effect at the time therein specified or, if no time is specified,
immediately; and, unless otherwise specified in such notice, the acceptance of such resignation
shall not be necessary to make it effective. Except as otherwise required by applicable law and
subject to the rights, if any, of the holders of shares of preferred stock then outstanding, any
director or the entire Board of Directors may be removed from office at any time, but only for
cause and only by the affirmative vote of the holders of at least two-thirds of the voting power of
the Corporation’s then issued and outstanding capital stock entitled to vote generally at an
election of directors of the Corporation.

     Section 7. Quorum. Except as otherwise required by law or the Articles of
Incorporation, at all meetings of the Board of Directors, a majority of the entire Board of
Directors shall constitute a quorum for the transaction of business and the act of a majority of
the directors present at any
meeting at which there is a quorum shall be the act of the Board of Directors. If a quorum
shall not be present at any meeting of the Board of Directors, the directors present thereat may
adjourn the meeting from time to time, without notice other than announcement at the meeting of the
time and place of the adjourned meeting, until a quorum shall be present.

     Section 8. Actions of the Board by Written Consent. Unless otherwise provided in the
Articles of Incorporation or these Bylaws, any action required or permitted to be taken at any
meeting of the Board of Directors or of any committee thereof may be taken without a meeting, if
all the members of the Board of Directors or committee, as the case may be, consent thereto in
writing or by electronic transmission, and the writing or writings or electronic transmission or
transmissions are delivered to the Corporation. The written action shall be

14

 

effective when signed
by all directors and delivered to the Corporation, unless a different effective time is provided in
the written action.

     Section 9. Meetings by Means of Conference Telephone. Unless otherwise provided in
the Articles of Incorporation or these Bylaws, members of the Board of Directors of the
Corporation, or any committee thereof, may participate in a meeting of the Board of Directors or
such committee by means of a conference telephone or other communications equipment by means of
which all persons participating in the meeting can hear each other, and participation in a meeting
pursuant to this Section 9 shall constitute presence in person at such meeting.

     Section 10. Committees. The Board of Directors, by resolution adopted by the
affirmative vote of a majority of all of the directors then in office, may designate one or more
committees, each committee to consist of one or more of the directors of the Corporation. The
Board of Directors
may appoint one or more directors as alternate members of any committee to replace any absent
or disqualified member at any meeting of such committee during the member’s absence or
disqualification. In the event of the absence or disqualification of a member of a committee, the
member or members present at any meeting of such committee and not disqualified from voting,
unanimously, may appoint another director to act in place of the absent or disqualified member.
Any committee, to the extent permitted by law and provided in the resolution establishing such
committee, shall have and may exercise all the powers and authority of the Board of Directors in
the management of the business and affairs of the Corporation. Each committee shall keep regular
minutes and report to the Board of Directors when required.

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     Section 11. Compensation. The directors may be paid their expenses, if any, of
attendance at each meeting of the Board of Directors and may be paid a fixed sum for attendance at
each meeting of the Board of Directors or a stated salary for service as director, payable in cash
or securities. No such payment shall preclude any director from serving the Corporation in any
other capacity and receiving compensation therefor. Members of special or standing committees may
be allowed like compensation for service as committee members.

     Section 12. Directors’ Assent. A director who is present at a meeting of the Board of
Directors or a committee of the Board of Directors when corporate action is taken is deemed to have
assented to the action taken unless: (i) the director objects at the beginning of the meeting, or
promptly upon arrival, to holding it or transacting business at the meeting; (ii) the director’s
dissent or abstention from the action taken is entered in the minutes of the meeting; or (iii) the
director delivers written notice of dissent or abstention to the presiding officer of the meeting
before its adjournment or to the
Corporation immediately after adjournment of the meeting. The right of dissent or abstention
is not available to a director who votes in favor of the action taken.

ARTICLE IV

OFFICERS

     Section 1. General. The officers of the Corporation shall be chosen by the Board of
Directors and shall be a Chief Executive Officer, a President, a Chief Financial Officer, a
Corporate Secretary and a Treasurer. The Board of Directors, in its discretion, also may choose a
Chairman of the Board of Directors (who must be a director) and one or more Vice Presidents,
Assistant Corporate Secretaries, Assistant Treasurers and other officers. Any number of offices
may be held by the same person, unless otherwise prohibited by law, the Articles of Incorporation
or these Bylaws. The officers of the Corporation need not be shareholders of the

16

 

Corporation nor,
except in the case of the Chairman of the Board of Directors, need such officers be directors of
the Corporation.

     Section 2. Election. The Board of Directors, at its first meeting held after each
Annual Meeting of Shareholders, shall elect the officers of the Corporation who shall hold their
offices for such terms and shall exercise such powers and perform such duties as shall be
determined from time to time by the Board of Directors; and each officer of the Corporation shall
hold office until such officer’s successor is elected and qualified, or until such officer’s
earlier death, resignation or removal. Any officer elected by the Board of Directors may be
removed at any time by the Board of Directors, although such removal shall be without prejudice to
the contract rights, if any, of the person so removed. Election or appointment of an officer or
agent shall not of itself
create contract rights. Any vacancy occurring in any office of the Corporation shall be
filled by the Board of Directors.

     Section 3. Voting Securities Owned by the Corporation. Powers of attorney, proxies,
waivers of notice of meeting, consents and other instruments relating to securities owned by the
Corporation may be executed in the name of and on behalf of the Corporation by the President or any
Vice President or any other officer authorized to do so by the Board of Directors and any such
officer may, in the name of and on behalf of the Corporation, take all such action as any such
officer may deem advisable to vote in person or by proxy at any meeting of security holders of any
corporation in which the Corporation may own securities and at any such meeting shall possess and
may exercise any and all rights and power incident to the ownership of such securities and which,
as the owner thereof, the Corporation might have exercised and possessed if present. The Board of
Directors may, by resolution, from time to time confer like powers upon any other person or
persons.

17

 

     Section 4. Chairman of the Board of Directors. The Chairman of the Board of
Directors, if there be one, shall preside at all meetings of the shareholders and of the Board of
Directors. Except where by law the signature of the President is required, the Chairman of the
Board of Directors shall possess the same power as the President to sign all contracts,
certificates and other instruments of the Corporation which may be authorized by the Board of
Directors. During the absence or disability of the Chief Executive Officer, the Chairman of the
Board of Directors shall exercise all the powers and discharge all the duties of the Chief
Executive Officer. The Chairman of the Board of Directors shall also perform such other duties and
may exercise such other powers as may from time to time be assigned by these Bylaws or by the Board
of Directors.

     Section 5. Chief Executive Officer

     The Chief Executive Officer shall, subject to the control of the Board of Directors, have
general supervision of the business of the Corporation and shall see that all orders and
resolutions of the Board of Directors are carried into effect. Except where by law the signature
of the President is required, the Chief Executive Officer shall possess the same power as the
President to sign all contracts, certificates and other instruments of the Corporation which may be
authorized by the Board of Directors. In the absence or disability of the Chairman of the Board of
Directors, or if there be none, the Chief Executive Officer shall preside at all meetings of the
shareholders and, provided the Chief Executive Officer is also a director, the Board of Directors.

     Section 6. President. The President shall, subject to the control of the Board of
Directors, the Chief Executive Officer and, if there be one, the Chairman of the Board of
Directors, have responsibility and authority for management of the day-to-day operations of the

18

 

Corporation. The President shall execute all bonds, mortgages, contracts and other instruments of
the Corporation, except where required or permitted by law to be otherwise signed and executed and
except that the other officers of the Corporation may sign and execute documents when so authorized
by these Bylaws, the Board of Directors or the President or Chief Executive Officer. At the
request of the Chief Executive Officer or in the Chief Executive Officer’s absence or in the event
of the Chief Executive Officer’s inability or refusal to act (and if there be no Chairman of the
Board of Directors), the President shall perform the duties of the Chief Executive Officer, and
when so acting, shall have all the powers of and be subject to all the restrictions upon the Chief
Executive Officer. The President shall also perform such other duties and may exercise
such other powers as may from time to time be assigned to such officer by these Bylaws, the
Board of Directors or the Chief Executive Officer.

     Section 7. Chief Financial Officer. The Chief Financial Officer, if there be one,
shall, subject to the control of the Board of Directors and the Chairman of the Board of Directors,
if there be one, have the responsibility for the financial affairs of the Corporation and shall
exercise supervisory responsibility for the performance of the duties of the Treasurer and the
controller, if any, of the Corporation. The Chief Financial Officer shall also perform such other
duties and may exercise such other powers as may from time to time be assigned to such officer by
these Bylaws or by the Board of Directors.

     Section 8. Vice Presidents. At the request of the Chief Executive Officer or
President or in the President’s absence or in the event of the President’s inability or refusal to
act (and if there be no Chairman of the Board of Directors and no Chief Executive Officer), the
Vice President, or the Vice Presidents if there are more than one (in the order designated by the
Board of Directors), shall perform the duties of the President, and when so acting, shall have all
the

19

 

powers of and be subject to all the restrictions upon the President. Each Vice President shall
perform such other duties and have such other powers as the Board of Directors from time to time
may prescribe. If there be no Chairman of the Board of Directors, no Chief Executive Officer and
no Vice President, the Board of Directors shall designate the officer of the Corporation who, in
the absence of the President or in the event of the inability or refusal of the President to act,
shall perform the duties of the President, and when so acting, shall have all the powers of and be
subject to all the restrictions upon the President.

     Section 9. Corporate Secretary. The Corporate Secretary shall attend all meetings of
the Board of Directors and all meetings of the shareholders and record all the proceedings thereat
in a book or books to be kept for that purpose. The Corporate Secretary shall also perform like
duties for committees of the Board of Directors when required. The Corporate Secretary shall give,
or cause to be given, notice of all meetings of the shareholders and special meetings of the Board
of Directors, and shall perform such other duties as may be prescribed by the Board of Directors,
the Chairman of the Board of Directors, if there be one, or the Chief Executive Officer, under
whose supervision the Corporate Secretary shall be. If the Corporate Secretary shall be unable or
shall refuse to cause to be given notice of all meetings of the shareholders and special meetings
of the Board of Directors, and if there be no Assistant Corporate Secretary, then either the Board
of Directors or the Chief Executive Officer may choose another officer to cause such notice to be
given. The Corporate Secretary shall see that all books, reports, statements, certificates and
other documents and records required by law to be kept or filed are properly kept or filed, as the
case may be.

     Section 10. Treasurer. The Treasurer shall have the custody of the corporate funds
and securities and shall keep full and accurate accounts of receipts and disbursements in

20

 

books
belonging to the Corporation and shall deposit all moneys and other valuable effects in the name
and to the credit of the Corporation in such depositories as may be designated by the Board of
Directors. The Treasurer shall disburse the funds of the Corporation as may be ordered by the
Board of Directors, taking proper vouchers for such disbursements, and shall render to the Chief
Financial Officer and Chief Executive Officer and the Board of Directors, at its regular meetings,
or when the Board of Directors so requires, an account of all transactions as Treasurer and of the
financial
condition of the Corporation. If required by the Board of Directors, the Treasurer shall give
the Corporation a bond in such sum and with such surety or sureties as shall be satisfactory to the
Board of Directors for the faithful performance of the duties of the office of the Treasurer and
for the restoration to the Corporation, in case of the Treasurer’s death, resignation, retirement
or removal from office, of all books, papers, vouchers, money and other property of whatever kind
in the Treasurer’s possession or under the Treasurer’s control belonging to the Corporation.

     Section 11. Assistant Corporate Secretaries. Assistant Corporate Secretaries, if
there be any, shall perform such duties and have such powers as from time to time may be assigned
to them by the Board of Directors, the Chief Executive Officer, the President, any Vice President,
if there be one, or the Corporate Secretary, and in the absence of the Corporate Secretary or in
the event of the Corporate Secretary’s inability or refusal to act, shall perform the duties of the
Corporate Secretary, and when so acting, shall have all the powers of and be subject to all the
restrictions upon the Corporate Secretary.

     Section 12. Assistant Treasurers. Assistant Treasurers, if there be any, shall
perform such duties and have such powers as from time to time may be assigned to them by the Board
of Directors, the Chief Executive Officer, the President, any Vice President, if there be

21

 

one, or
the Treasurer, and in the absence of the Treasurer or in the event of the Treasurer’s inability or
refusal to act, shall perform the duties of the Treasurer, and when so acting, shall have all the
powers of and be subject to all the restrictions upon the Treasurer. If required by the Board of
Directors, an Assistant Treasurer shall give the Corporation a bond in such sum and with such
surety or sureties as shall be satisfactory to the Board of Directors for the faithful performance
of the
duties of the office of Assistant Treasurer and for the restoration to the Corporation, in
case of the Assistant Treasurer’s death, resignation, retirement or removal from office, of all
books, papers, vouchers, money and other property of whatever kind in the Assistant Treasurer’s
possession or under the Assistant Treasurer’s control belonging to the Corporation.

     Section 13. Other Officers. Such other officers as the Board of Directors may choose
shall perform such duties and have such powers as from time to time may be assigned to them by the
Board of Directors. The Board of Directors may delegate to any other officer of the Corporation
the power to choose such other Vice Presidents, Assistant Corporate Secretaries, Assistant
Treasurers and other officers and to prescribe their respective duties and powers in accordance
with these Bylaws.

ARTICLE V

STOCK

     Section 1. Form of Certificates. Every holder of stock in the Corporation shall be
entitled to have a certificate signed by, or in the name of, the Corporation by the (i) Chairman of
the Board of Directors (if there be one), the President or a Vice President and (ii) Treasurer or
an Assistant Treasurer, or the Corporate Secretary or an Assistant Corporate Secretary, certifying
the number and class of shares and the designation of the series, if any, the certificate
represents.

22

 

     Section 2. Signatures. Any or all of the signatures on a certificate may be a
facsimile. In case any officer, transfer agent or registrar who has signed or whose facsimile
signature has been placed upon a certificate shall have ceased to be such officer, transfer agent
or registrar before such certificate is issued, such certificate shall be nevertheless valid.

     Section 3. Lost Certificates. The Board of Directors may direct a new certificate to
be issued in place of any certificate theretofore issued by the Corporation alleged to have been
lost, stolen or destroyed, upon the making of an affidavit of that fact by the person claiming the
certificate of stock to be lost, stolen or destroyed. When authorizing such issue of a new
certificate, the Board of Directors may, in its discretion and as a condition precedent to the
issuance thereof, require the owner of such lost, stolen or destroyed certificate, or such owner’s
legal representative, to advertise the same in such manner as the Board of Directors shall require
and/or to give the Corporation a bond in such sum as it may direct as indemnity against any claim
that may be made against the Corporation on account of the alleged loss, theft or destruction of
such certificate or the issuance of such new certificate.

     Section 4. Transfers. Stock of the Corporation shall be transferable in the manner
prescribed by applicable law and in these Bylaws. Transfers of stock shall be made on the books of
the Corporation only by the person named in the certificate or by such person’s attorney lawfully
constituted in writing and upon the surrender of the certificate therefor, properly endorsed for
transfer and payment of all necessary transfer taxes; provided, however, that such
surrender and endorsement or payment of taxes shall not be required in any case in which the
officers of the Corporation shall determine to waive such requirement. Every certificate
exchanged, returned or surrendered to the Corporation shall be marked “Cancelled,” with the date of
cancellation, by the Corporate Secretary or Assistant Corporate Secretary or the

23

 

transfer agent
thereof. No transfer of stock shall be valid as against the Corporation for any purpose until it
shall have been entered in the stock records of the Corporation by an entry showing from and to
whom transferred.

     Section 5. Dividend Record Date. In order to determine the shareholders entitled to
receive payment of any dividend or other distribution or allotment of any rights or the
shareholders entitled to exercise any rights in respect of any change, conversion or exchange of
stock, or for the purpose of any other lawful action, the Board of Directors may fix a future date
as the record date, which record date shall not be not more than seventy (70) days prior to such
action. If the Board of Directors does not fix the record date for determining shareholders
entitled to a distribution, other than one involving a purchase, redemption or other acquisition
of the Corporation’s shares, the record date shall be the date the Board of Directors authorizes
the distribution.

     Section 6. Record Owners. The Corporation shall be entitled to recognize the
exclusive right of a person registered on its books as the owner of shares to receive dividends,
and to vote as such owner, and to hold liable for calls and assessments a person registered on its
books as the owner of shares, and shall not be bound to recognize any equitable or other claim to
or interest in such share or shares on the part of any other person, whether or not it shall have
express or other notice thereof, except as otherwise required by law.

     Section 7. Transfer and Registry Agents. The Corporation may from time to time
maintain one or more transfer offices or agencies and registry offices or agencies at such place or
places as may be determined from time to time by the Board of Directors.

24

 

ARTICLE VI

GENERAL PROVISIONS

     Section 1. Dividends. The Board of Directors may from time to time declare, and the Corporation may pay,
dividends on outstanding shares of the Corporation to its shareholders in the manner and upon the
terms and conditions provided by applicable law and the Articles of Incorporation.

     Section 2. Disbursements. All checks or demands for money and notes of the
Corporation shall be signed by such officer or officers or such other person or persons as the
Board of Directors may designate from time to time.

     Section 3. Fiscal Year. The fiscal year of the Corporation shall be fixed by
resolution of the Board of Directors.

ARTICLE VII

INDEMNIFICATION

     Section 1. Director and Officer Indemnification; Advancement of Expenses. The
Corporation shall indemnify its directors and officers to the fullest extent authorized or
permitted by law, as now or hereafter in effect, and such right to indemnification shall continue
as to a person who has ceased to be a director or officer of the Corporation and shall inure to the
benefit of his or her heirs, executors and personal and legal representatives; provided,
however, that, except for proceedings to enforce rights to indemnification, the Corporation
shall not be obligated to indemnify any director or officer (or his or her heirs, executors or
personal or legal representatives) in connection with a proceeding (or part thereof) initiated by
such person unless such proceeding (or part thereof) was authorized or consented to by the Board of
Directors. The right to indemnification conferred by this Section 1 shall include the right to be
paid by the

25

 

Corporation the expenses incurred in defending or otherwise participating in any
proceeding in advance of its final disposition.

     Section 2. Survival of Indemnification and Advancement of Expenses. The
indemnification and advancement of expenses provided by, or granted pursuant to, this Article VII
shall, unless otherwise provided when authorized or ratified, continue as to a person who has
ceased to be a director or officer and shall inure to the benefit of the heirs, executors and
administrators of such a person.

     Section 3. Non-Exclusiveness. The indemnification and advancement of expenses
provided by this Article VII shall not be deemed exclusive of any other rights not prohibited by
law to which those seeking indemnification or advancement of expenses may be entitled as a matter
of law or under the Articles of Incorporation, these Bylaws, any agreement, vote of shareholders,
any insurance purchased by the Corporation, or otherwise, both as to action in the Indemnitee’s
official capacity and as to action in another capacity while holding such office, and shall
continue as to a person who has ceased to be a director, officer, employee or agent and shall inure
to the benefit of the heirs, executors and administrators of such a person.

     Section 4. Purchase of Insurance. The Corporation may purchase and maintain insurance
on behalf of an individual who is a director or officer of the Corporation, or who, while a
director or officer of the Corporation, serves at the Corporation’s request as a director, officer,
partner, trustee, employee or agent of another domestic or foreign corporation, partnership, joint
venture, trust, employee benefit plan or other entity, against liability asserted against or
incurred by the individual in that capacity or arising from the individual’s status as a director
or officer, whether or not the Corporation would have power to indemnify or advance

26

 

expenses to the
director or
officer against the same liability under the provisions of this Article VII or the South
Dakota Business Corporation Act.

     Section 5. Indemnification of Employees and Agents. The Corporation may, to the
extent authorized from time to time by the Board of Directors, provide rights to indemnification
and to the advancement of expenses to employees and agents of the Corporation similar to those
conferred in this Article VII to directors and officers of the Corporation.

ARTICLE VIII

AMENDMENTS

     Section 1. Amendments. In furtherance and not in limitation of the powers conferred
upon it by the laws of the State of South Dakota, the Board of Directors shall have the power to
adopt, amend, alter or repeal the Corporation’s Bylaws. The affirmative vote of at least a
majority of the entire Board of Directors shall be required to adopt, amend, alter, change or
repeal the Corporation’s Bylaws. The Corporation’s Bylaws may also be adopted, amended, altered,
changed or repealed by the affirmative vote of the holders of at least two-thirds of the voting
power of the Corporation’s then issued and outstanding capital stock entitled to vote generally at
an election of directors of the Corporation.

     Section 2. Entire Board of Directors. As used in this Article VIII and in these
Bylaws generally, the term “entire Board of Directors” means the total number of directors which
the Corporation would have if there were no vacancies.

* * * * *

27exv4w7

 

EXHIBIT
4.7

US BIOENERGY CORPORATION

2006 STOCK INCENTIVE PLAN

Adopted
by the Board of Directors on November 17, 2006

Approved by the Shareholders on
December 8, 2006

 

 

TABLE OF CONTENTS

	 	 	 	 	 	 	 
	 	 	 	 	Page
	SECTION 1.

	 	General Purpose of Plan; Definitions
	 	 	1	 
	 
	 	 	 	 	 	 
	SECTION 2.

	 	Administration
	 	 	6	 
	 
	 	 	 	 	 	 
	SECTION 3.

	 	Stock Subject to Plan
	 	 	7	 
	 
	 	 	 	 	 	 
	SECTION 4.

	 	Eligibility
	 	 	9	 
	 
	 	 	 	 	 	 
	SECTION 5.

	 	Option Awards
	 	 	9	 
	 
	 	 	 	 	 	 
	SECTION 6.

	 	Stock Appreciation Rights
	 	 	12	 
	 
	 	 	 	 	 	 
	SECTION 7.

	 	Restricted Stock and Restricted Stock Unit Awards
	 	 	14	 
	 
	 	 	 	 	 	 
	SECTION 8.

	 	Deferred Stock Awards
	 	 	16	 
	 
	 	 	 	 	 	 
	SECTION 9.

	 	Performance Stock, Director Stock and Other Awards
	 	 	16	 
	 
	 	 	 	 	 	 
	SECTION 10.

	 	Change in Control
	 	 	17	 
	 
	 	 	 	 	 	 
	SECTION 11.

	 	Additional Change in Control Provisions
	 	 	18	 
	 
	 	 	 	 	 	 
	SECTION 12.

	 	Substitute Awards
	 	 	18	 
	 
	 	 	 	 	 	 
	SECTION 13.

	 	General Provisions
	 	 	18	 
	 
	 	 	 	 	 	 
	SECTION 14.

	 	Amendments and Termination
	 	 	21	 
	 
	 	 	 	 	 	 
	SECTION 15.

	 	Governing Law
	 	 	21	 
	 
	 	 	 	 	 	 
	SECTION 16.

	 	Effective Date and Term of Plan
	 	 	21	 
	 
	 	 	 	 	 	 
	SECTION 17.

	 	Unfunded Status of Plan
	 	 	21	 

 

 

US BIOENERGY CORPORATION

2006 STOCK INCENTIVE PLAN

SECTION 1. General Purpose of Plan; Definitions.

     1.1 General Purpose. The name of the plan is the US BioEnergy Corporation 2006 Stock
Incentive Plan (the “Plan”). The purpose of the Plan is to enable US BioEnergy Corporation (the
“Company”) and its Subsidiaries to retain and attract executives, other employees, members of the
Board of Directors, and Consultants who contribute to the Company’s success by their ability,
ingenuity and industry, and to enable such individuals to participate in the long-term success and
growth of the Company by giving them a proprietary interest in the Company.

     1.2 Definitions. For purposes of the Plan, the following terms shall be defined as
set forth below:

     (a) “Agreement” or “Award Agreement” means an agreement by and between
the Company and a Recipient under the Plan setting forth the terms and conditions of an
Award.

     (b) “Award” means the grant of an Option, Restricted Stock, a Restricted Stock
Unit, unrestricted Stock, Performance Stock, Deferred Stock, Director Stock, a Stock
Appreciation Right, Other Award or any combination thereof, pursuant to the terms of the
Plan.

     (c) “Board” means the Board of Directors of the Company, as it may be comprised
from time to time.

     (d) “Cause” means, except as may otherwise be provided in the terms of the
Award or in a written employment agreement between the Company and the Recipient:

     (i) a material breach of any written employment, consulting or other agreement
between the Company and the Recipient;

     (ii) a material breach of any code of conduct established by the Company;

     (iii) commission of a felony by a Recipient; or

     (iv) the failure of a Recipient to contest prosecution for a felony, or a
Recipient’s willful misconduct, dishonesty, breach of fiduciary duty, or gross
negligence involving the business or reputation of the Company.

     (e) “Change in Control” means, except as may otherwise be provided in the terms
of the Award Agreement or in a written agreement between the Company and the Recipient, any
of the following:

1

 

     (i) Any “person” (as such term is used in Sections 13(d) and 14(d) of the
Securities Exchange Act) acquires or becomes a “beneficial owner” (as defined in
Rule 13d-3 or any successor rule under the Securities Exchange Act), directly or
indirectly, of securities of the Company representing 50% or more of the combined
voting power of the Voting Securities, provided, however, that the following shall
not constitute a Change in Control pursuant to this Section 1.2(e)(i):

	 	(A)	 	any acquisition of Voting Securities or Stock
of the Company directly from the Company other than in connection with
a transaction described in Section 1.2(e)(iii) of the Plan;
	 
	 	(B)	 	any acquisition or beneficial ownership by the
Company or a Subsidiary;
	 
	 	(C)	 	any acquisition or beneficial ownership by any
employee benefit plan (or related trust) sponsored or maintained by the
Company or one or more of its Subsidiaries;
	 
	 	(D)	 	any acquisition or beneficial ownership by any
corporation with respect to which, immediately following such
acquisition, more than 50% of the combined voting power of the
Company’s then outstanding Voting Securities and the Stock of the
Company is then beneficially owned, directly or indirectly, by all or
substantially all of the persons who beneficially owned Voting
Securities and Stock of the Company immediately prior to such
acquisition in substantially the same proportions as their ownership of
such Voting Securities and Stock, as the case may be, immediately prior
to such acquisition;

     (ii) A majority of the members of the Board of the Company shall not be
Continuing Directors;

     (iii) The consummation of a merger, consolidation or reorganization of the
Company or a statutory exchange of outstanding Voting Securities of the Company,
unless, immediately following such merger, consolidation, reorganization or
exchange, all or substantially all of the persons who were the beneficial owners,
respectively, of Voting Securities and Stock of the Company immediately prior to
such reorganization, merger, consolidation or exchange beneficially own, directly or
indirectly, more than 50% of, respectively, the combined voting power of the then
outstanding voting securities entitled to vote generally in the election of
directors and the then outstanding shares of common stock, as the case may be, of
the corporation resulting from such reorganization, merger, consolidation or
exchange in substantially the same proportions as their ownership immediately prior
to such reorganization, merger, consolidation or exchange, of the Voting Securities
and Stock of the Company, as the case may be; or

2

 

     (iv) Approval by the shareholders of the Company of (x) a complete liquidation
or dissolution of the Company or (y) the consummation of the sale or other
disposition of all or substantially all of the assets of the Company (in one or a
series of transactions), other than to a corporation with respect to which,
immediately following such sale or other disposition, more than 50% of,
respectively, the combined voting power of the then outstanding voting securities of
such corporation entitled to vote generally in the election of directors and the
then outstanding shares of common stock of such corporation is then beneficially
owned, directly or indirectly, by all or substantially all of the persons who were
the beneficial owners, respectively, of the Voting Securities and Stock of the
Company immediately prior to such sale or other disposition in substantially the
same proportions as their beneficial ownership immediately prior to such sale or
other disposition, of the Voting Securities and Stock of the Company, as the case
may be.

     (f) “Code” means the Internal Revenue Code of 1986, as amended from time to
time, or any successor statute.

     (g) “Committee” means the Committee referred to in Section 2.1 of the Plan.

     (h) “Company” means US BioEnergy Corporation, a corporation organized under the
laws of the State of South Dakota (or any successor corporation).

     (i) “Consultant” means any natural person providing bona fide services to the
Company or a Parent Corporation or a Subsidiary of the Company (other than persons either
providing services in connection with the offer or sale of securities in a capital raising
transaction or directly or indirectly promoting or maintaining a market for the Company’s
Stock), who is compensated for such services and who is not an employee of the Company or
any Parent Corporation or Subsidiary of the Company. A “Consultant” includes a Non-Employee
Director.

     (j) “Continuing Directors” means:

     (i) individuals who, on the date hereof, are directors of the Company;

     (ii) individuals elected as directors of the Company subsequent to the date
hereof for whose election proxies shall have been solicited by the Board; or

     (iii) any individual elected or appointed by the Board to fill vacancies on the
Board caused by death or resignation (but not by removal) or to fill newly-created
directorships;

provided, however, that a Continuing Director shall not include a director whose initial
assumption of office is in connection with an actual or threatened election contest,
including, but not limited to, a consent solicitation, relating to the election of directors
of the Company.

3

 

     (k) “Deferred Stock” means an Award made pursuant to Section 8 of the Plan of
the right to receive Stock at the end of a specified deferral period or upon the achievement
of specified performance criteria.

     (l) “Director Stock” means an Award made pursuant to Section 9.2 of the Plan.

     (m) “Disability” means, except as may otherwise be provided in the terms of an
Award Agreement or in a written agreement between the Company and the Recipient, the
Recipient:

     (i) is unable to engage in any substantial gainful activity by reason of any
medically determinable physical or mental impairment which can be expected to result
in death or can be expected to last for a continuous period of not less than 12
months;

     (ii) is, by reason of any medically determinable physical or mental impairment
which can be expected to result in death or can be expected to last for a continuous
period of not less than 12 months, receiving income replacement benefits for a
period of not less than three months under an accident and health plan covering
employees of the Company;

     (iii) when used in connection with the exercise of an Incentive Stock Option
following termination of employment, has a disability within the meaning of Section
22(e)(3) of the Code;

     (iv) solely to the extent necessary to satisfy Section 409A of the Code, has a
“disability” or is “disabled” within the meaning of Section 409A of the Code.

     (n) “Effective Date” shall have the meaning set forth in Section 16 of the
Plan.

     (o) “Fair Market Value” of Stock on any given date shall be determined by the
Committee as follows (but in no event shall “Fair Market Value” be less than fair market
value within the meaning of Section 409A of the Code):

     (i) if the Stock is listed for trading on one or more national securities
exchanges, or is traded on the Nasdaq Stock Market (including the Nasdaq Small Cap
Market), the last reported sales price on such national securities exchange or the
Nasdaq Stock Market on the day prior to the date in question, or if such Stock shall
not have been traded on such principal exchange on such date, the last reported
sales price on such principal exchange on the first day prior thereto on which such
Stock was so traded; or

     (ii) if the Stock is not listed for trading on a national securities exchange
or the Nasdaq Stock Market, the NASDAQ Global Market, or any successor market, but
is traded on the over-the-counter market, including the Nasdaq OTC Bulletin Board,
the closing bid price for such Stock on the day prior to the date in question, or if
there is no closing bid price for such Stock on such

4

 

date, the closing bid price on the first day prior thereto on which such price
existed; or

     (iii) if neither (i) nor (ii) is applicable, by any means fair and reasonable
determined, in good faith, by the Committee, which determination shall be final and
binding on all parties.

     (p) “Incentive Stock Option” means any Award intended to be and designated as
an “Incentive Stock Option” within the meaning of Section 422 of the Code and that satisfies
the requirements set forth therein.

     (q) “Non-Employee Director” means a non-employee director within the meaning of
Rule 16b-3 under the Securities Exchange Act.

     (r) “Non-Qualified Option” means any Option that is not an Incentive Stock
Option.

     (s) “Option” means any Award to purchase Stock granted pursuant to Section 5 of
the Plan.

     (t) “Other Award” means any Award granted pursuant to Section 9.3 of the Plan.

     (u) “Outside Director” means a member of the Board who satisfies the
requirements of an outside director for purposes of Section 162(m) of the Code.

     (v) “Parent Corporation” means any corporation (other than the Company) in an
unbroken chain of corporations ending with the Company if each of the corporations (other
than the Company) owns stock possessing 50% or more of the total combined voting power of
all classes of stock in one of the other corporations in the chain.

     (w) “Recipient” means any eligible person to whom an Award has been granted
under the Plan.

     (x) “Restricted Stock” means an Award of shares of Stock pursuant to Section 7
of the Plan that are subject to restrictions as described therein.

     (y) “Restricted Stock Unit” means an Award of the right to receive a share of
Stock granted pursuant to Section 7 of the Plan that are subject to restrictions as
described therein.

     (z) “Securities Exchange Act” means the Securities Exchange Act of 1934, as
amended from time to time, or any successor statute.

     (aa) “Stock” means the common stock, $0.01 par value per share, of the Company.

     (bb) “Stock Appreciation Right” means the right, pursuant to an Award granted
under Section 6 of the Plan, to surrender to the Company all or a portion of a right in

5

 

exchange for an amount or a number of shares of Stock equal to the difference between
(i) the aggregate Fair Market Value, as of the date the right or such portion thereof is
exercised and surrendered, of the shares of Stock covered by such right or such portion
thereof, and (ii) the aggregate exercise price of such right or such portion thereof on the
date such Award was made.

     (cc) “Subsidiary” means any corporation (other than the Company), foreign or
domestic, in an unbroken chain of corporations beginning with the Company if each of the
corporations (other than the last corporation in the unbroken chain) owns stock possessing
50% or more of the total combined voting power of all classes of stock in one of the other
corporations in the chain.

     (dd) “Voting Securities” means the Company’s then outstanding securities
entitled to vote generally in the election of directors.

SECTION 2. Administration.

     2.1 Authority. The Plan shall be administered by the Board or by a Committee
appointed by the Board consisting of at least two members of the Board, each of whom shall serve at
the pleasure of the Board. If at any time no Committee shall be in office, then the Board shall
exercise the functions of the Committee specified in the Plan. The Board may exercise any or all
of the functions of the Committee specified in the Plan, except that:

     (a) at such time as any Award is subject to the limitations under Section 162(m) of the
Code, the Plan shall be administered by a Committee consisting solely of Outside Directors;

     (b) at such time as the Company and its affiliates are subject to the limitations under
Section 16(b) of the Securities Exchange Act, the Committee shall consist solely of
Non-Employee Directors; and

     (c) to the extent applicable, the Plan shall be administered by a Committee that is
comprised solely of members who satisfy the applicable requirements of any stock exchange on
which the Stock may then be listed.

Subject to the foregoing, references in the Plan to the Committee shall also include the Board, to
the extent the context permits.

     2.2 Powers. The Committee shall have the power and authority to grant Awards pursuant
to the terms of the Plan. In particular, the Committee shall have the authority:

     (a) Recipients. To select Recipients to whom Awards may from time to time be
granted hereunder;

     (b) Amount. To determine the number of shares of Stock, units, or other
measures to be covered by each such Award granted hereunder;

6

 

     (c) Terms and Conditions. To determine the terms and conditions, not
inconsistent with the terms of the Plan, of any Award granted hereunder (including, but not
limited to, any restriction on any Award and/or the Stock relating thereto);

     (d) Amendment; Acceleration. To amend the terms of any Award theretofore
granted, prospectively or retroactively, to the extent such amendment is consistent with the
terms of the Plan, including to accelerate the date on which any Award becomes exercisable
or vested and to accelerate the lapse of restrictions on any Award; provided that no such
amendment or action shall impair the rights of any Recipient without his or her consent
except to the extent authorized under the Plan;

     (e) Substitution. To substitute new Awards for previously granted Awards,
provided, however that substituting new Awards for previously granted Options having higher
exercise prices shall not be permitted without shareholder approval; 

     (f) Determination. To make any other determination and take any other action
that the Committee deems necessary or desirable for the administration of the Plan; and

     (g) Rules. To adopt, alter and repeal such administrative rules, guidelines
and practices governing the Plan as it shall, from time to time, deem advisable; to
interpret the terms and provisions of the Plan and any Award issued under the Plan (and any
agreements relating thereto) and to otherwise supervise the administration of the Plan.

     (h) Binding Authority; Limitation on Liability. All decisions made by the
Committee pursuant to the provisions of the Plan shall be final, conclusive and binding on
all persons, including the Company and the Recipients. No member of the Board or the
Committee, nor any officer or employee of the Company acting on behalf of the Board or the
Committee, shall be personally liable for any action, determination, or interpretation taken
or made in good faith with respect to the Plan, and all members of the Board or the
Committee and each and any officer or employee of the Company acting on their behalf shall,
to the extent permitted by law, be fully indemnified and protected by the Company in respect
of any such action, determination or interpretation.

     2.3 Delegation. Except to the extent prohibited by applicable law or the applicable
rules of a stock exchange, the Committee may delegate the authority to exercise the powers
specified in Section 2.2 to any officer of the Company, provided, however, that such authority
shall not be exercised by any officer with respect to persons who are either the chief executive
officer, chief financial officer, or any other executive officer of the Company or with respect to
any director of the Company.

     2.4 Decisions Binding. All decisions made by the Committee (or its delegate to the
extent provided in Section 2.3) pursuant to the provisions of the Plan shall be final and binding
on all persons, including the Company and all Recipients.

SECTION 3. Stock Subject to Plan.

     3.1 Shares Reserved for Issuance. The total number of shares of Stock reserved and
available for distribution under the Plan shall be 6,560,943,

7

 

minus the number of shares subject to options or other awards granted under the 2005 Stock
Incentive Plan as of such effective date (such total number of shares subject to adjustment as
provided in Section 3.3), all of which may be issued as Incentive Stock Options. Such shares shall
consist of, in whole or in part, authorized and unissued shares of Stock or treasury shares of the
Company.

     3.2 Share Counting. If any shares of Stock become available as a result of canceled,
unexercised, lapsed or terminated Awards under the Plan, such shares shall again be available for
distribution in connection with future Awards under the Plan. Upon a stock-for-stock exercise of
an Award, the withholding of Stock for the payment of the exercise price of an Award, or upon the
withholding of Stock for the payment of taxes on an Award, only the net number of shares of Stock
issued to the Recipient shall be used to calculate the number of shares remaining available for
distribution under the Plan. The grant of any Stock Appreciation Rights that may be settled only
in cash shall not reduce the number of shares of Stock with respect to which Awards may be granted
pursuant to the Plan and, upon exercise of a Stock Appreciation Right, only the number of shares of
Stock actually issued under the Stock Appreciation Right (and not the number of shares of Stock
with respect to which the Stock Appreciation Right is granted) shall reduce the number of shares of
Stock with respect to which Awards may be granted pursuant to the Plan.

     3.3 Adjustments. In the event of a corporate transaction involving the Company
(including, without limitation, any merger, reorganization, consolidation, recapitalization, stock
dividend, stock split, other change in corporate structure affecting the Stock, or spin-off or
other distribution of assets to shareholders) or other event affecting the Company or any class of
Stock which would be reasonably likely to result in the diminution or enlargement of any of the
benefits intended to be made available under the Plan or an Award, the Committee shall, without the
consent of any Recipient, make such adjustments as it determines in its discretion to be equitable
and appropriate as to the number and kind of shares of Stock subject to and reserved under the
Plan, including any limits on shares established under the Plan and the exercise or purchase price
of each share subject to an Award, and the number and kind of securities issuable upon exercise,
payment or settlement of an Award; provided that the number of shares of Stock subject to any Award
shall always be a whole number. Without limiting the generality of the foregoing, in connection
with any transaction described in the foregoing sentence, the Committee may provide, for the
cancellation of any outstanding Awards in exchange for payment in cash or other property of the
Fair Market Value of the shares of Stock or units covered by such Awards reduced, by the exercise
or purchase price thereof, to the extent applicable.

     3.4 Effect of Award. The grant of an Award pursuant to the Plan shall not limit in
any way the right or power of the Company to make adjustments, reclassifications, reorganizations
or changes of its capital or business structure or to merge, exchange or consolidate or to
dissolve, liquidate or transfer all or any part of its business or assets.

     3.5 Application of Code Section 409A. If and to the extent that any provision of an
Award is required to comply with Section 409A of the Code, such provision shall be administered and
interpreted in a manner consistent with the requirements of such Section. If

8

 

and solely to the extent that such provision as currently written would conflict with Section
409A of the Code, the Committee shall have the authority, without the consent of the Recipient, to
administer such provision and to amend the Award with respect to such provision to the extent the
Committee deems necessary for the purposes of avoiding any portion of amounts owed to the Recipient
being retroactively included in the taxable income of the Recipient for any prior taxable year.

SECTION 4. Eligibility.

     Officers, other employees of the Company and its Subsidiaries, members of the Board, and
Consultants who are responsible for or contribute to the management, growth and/or profitability of
the business of the Company and its Subsidiaries are eligible to be granted Awards under the Plan.
Recipients under the Plan shall be selected from time to time by the Committee, in its sole
discretion or as otherwise provided in Section 2.3, from among those eligible.

SECTION 5. Option Awards.

     5.1 Option Types. Each Option shall be evidenced by a written Agreement, in such form
as the Committee may approve from time to time, which Agreement shall be subject to the provisions
of the Plan and to such other terms and conditions as the Committee may deem appropriate. The
Options granted under the Plan may be of two types: (i) Incentive Stock Options and (ii)
Non-Qualified Options. No Incentive Stock Option may be issued more than 10 years after the
earlier of the date the Plan is adopted by the Board or is approved by the shareholders of the
Company.

     5.2 Non-Qualified Options. To the extent that any Option or portion of an Option does
not qualify as an Incentive Stock Option, it shall constitute a separate Non-Qualified Option.

     5.3 Incentive Stock Options; Interpretation. Notwithstanding anything in the Plan to
the contrary, but subject to the following sentence, no term of the Plan relating to an Incentive
Stock Option shall be interpreted, amended or altered, nor shall any discretion or authority
granted under the Plan be so exercised, so as to disqualify either the Plan or any Incentive Stock
Option under Section 422 of the Code. The preceding sentence, however, shall not preclude any
modification or amendment to an outstanding Incentive Stock Option, whether or not such
modification or amendment results in disqualification of such Option as an Incentive Stock Option,
to the extent that the Committee determines that such modification or amendment is necessary or
appropriate. Incentive Stock Options may be granted solely to employees of the Company or any of
the Company’s parent or subsidiary corporations (in each case, within the meaning Section 424 of
the Code), or of a corporation or a parent or subsidiary corporation of such corporation issuing or
assuming, or that has issued or assumed, a stock option in a transaction in which Section 424(a) of
the Code applies.

     5.4 Terms and Conditions. Options granted under the Plan shall be subject to the
following terms and conditions and shall contain such additional terms and conditions, not
inconsistent with the terms of the Plan, as the Committee shall deem desirable:

9

 

     (a) Limitation under Section 162(m) of the Code. At such time as any Option
under the Plan granted by the Committee is subject to the limitations under Section 162(m)
of the Code, no Recipient shall receive grants of Options and Stock Appreciation Rights
under the Plan that exceed an aggregate of 1,000,000 shares of Stock during any fiscal year
of the Company.

     (b) Annual Limit on Incentive Stock Options. The aggregate Fair Market Value
(determined as of the time the Option is granted) of the Stock with respect to which an
Incentive Stock Option under the Plan or any other plan of the Company or any Subsidiary or
Parent Corporation is exercisable for the first time by a person during any calendar year
shall not exceed $100,000. To the extent any Option is exercisable in excess of the
foregoing limit in any calendar year, such Option shall be a Non-Qualified Stock Option.

     (c) Option Exercise Price. The exercise price per share of Stock purchasable
under an Option shall be determined by the Committee at the time of grant, except that the
exercise price of an Option shall not be less than 100% of the Fair Market Value of the
Stock on the date of grant of such Option. If an employee owns or is deemed to own (by
reason of the attribution rules applicable under Section 424(d) of the Code) more than 10%
of the combined voting power of all classes of capital stock of the Company or any Parent
Corporation or Subsidiary and an Incentive Stock Option is granted to such employee, the
Option exercise price shall be no less than 110% of the Fair Market Value of the Stock on
the date of grant of such Option. In the event the Committee does not fix the exercise price
of the Option, the exercise price shall be 100% of Fair Market Value on the date of grant or
as provided in the preceding sentence.

     (d) Option Term. The Committee shall fix the term of each Option, except that
no Incentive Stock Option shall be exercisable more than ten years after the date of grant
of such Option (except as provided in the next sentence). If an employee owns or is deemed
to own (by reason of the attribution rules of Section 424(d) of the Code) more than 10% of
the combined voting power of all classes of capital stock of the Company or any Parent
Corporation or Subsidiary and an Incentive Stock Option is granted to such employee, the
term of such Option shall be no more than five years from the date of grant of such Option.
In the event that the Committee does not fix the term of an Option, the term shall be ten
years from the date the Option is granted or as otherwise provided in the preceding
sentence, subject to earlier termination as otherwise provided herein.

     (e) Exercisability. An Option shall be exercisable in accordance with such
terms and conditions and during such periods as determined by the Committee at or after
grant, subject to the restrictions stated in Section 5.4(b) above. In the event the
Committee does not determine the time at which an Option shall become exercisable, such
Option shall be exercisable in equal installments of 20% of the shares of Stock subject to
the Option on and after the first anniversary of the date of grant of the Option and an
additional 20% of the shares of Stock subject to the Option on and after the second, third,
fourth and fifth anniversaries of the date of grant of the Option, subject to earlier
termination as otherwise provided herein. Notwithstanding anything in the Plan to the
contrary, no Option shall be exercisable after the expiration of its term.

10

 

     (f) Method of Exercise. An Option may be exercised in whole or in part at any
time during the Option term by giving written notice of exercise to the Company, specifying
the number of shares of Stock to be purchased. Such notice shall be accompanied by payment
in full of the exercise price, either by certified or bank check, or by any other form of
legal consideration deemed sufficient by the Committee and consistent with the Plan’s
purpose and applicable law, including, to the extent permitted by applicable law, delivery
of irrevocable instructions to a broker acceptable to the Company to promptly deliver to the
Company the amount of sale or loan proceeds to pay the entire exercise price and any tax
withholding resulting from such exercise. As determined by the Committee at the time of
grant or exercise, in its sole discretion, payment in full or in part may also be made by
tendering, by either actual delivery of Stock or attestation, Stock already owned by the
Recipient for a period of time greater than six months and that is valued at Fair Market
Value as of such time; provided, however, that, in the case of an Incentive Stock Option,
the right to make a payment in the form of already owned shares of Stock may be authorized
only at the time the Option is granted. No Stock shall be issued until full payment
therefor has been made. A Recipient shall generally have the rights to dividends and other
rights of a shareholder with respect to Stock subject to the Option when the Recipient has
given written notice of exercise, has paid in full for such Stock, and, if requested, has
given the representation described in Section 13.1.

     (g) Transferability of Options.

     (i) No Incentive Stock Option shall be transferable by the Recipient otherwise
than by will or by the laws of descent and distribution, and all Incentive Stock
Options shall be exercisable, during the Recipient’s lifetime, only by the
Recipient.

     (ii) The Committee may, in its discretion, authorize all or a portion of any
Non-Qualified Option to be granted to a Recipient to be on terms which permit
transfer by such Recipient to: (A) the spouse, children or grandchildren of the
Recipient (“Immediate Family Members”), (B) a trust or trusts for the exclusive
benefit of such Immediate Family Members, or (C) a partnership or partnerships in
which such Immediate Family Members are the only partners, provided that: (1) there
may be no consideration for any such transfer, (2) the Option pursuant to which such
Stock is granted must be approved by the Committee, and must expressly provide for
transferability in a manner consistent with this Section 5.4(g)(ii), and (3)
subsequent transfers of a transferred Option shall be prohibited. Following
transfer, any such Option shall continue to be subject to the same terms and
conditions as were applicable immediately prior to transfer, provided that the term
“Recipient” herein shall in such event be deemed to refer to the transferee, except
that the events of termination of employment and the provisions of Sections 5.4(h)
and (i) hereof shall continue to be applied with respect to the original Recipient,
following which the Option shall be exercisable by the transferee only to the
extent, and for the periods specified in such Sections.

11

 

     (iii) Non-Qualified Options may be transferred to the spouse or former spouse
of the Recipient to the extent provided in a domestic relations order issued in
accordance with applicable state law.

     (h) Termination by Death or Disability. Unless the Option Agreement provides
otherwise or the Committee determines, if a Recipient’s employment by, or service with, the
Company or any Subsidiary or Parent Corporation terminates by reason of death or Disability,
the Option may thereafter be exercised, to the extent it was exercisable at the time of
death or Disability (or on such accelerated basis as the Committee shall determine at or
after grant), by the Recipient or the legal representative of the estate or by the legatee
of the Recipient under the will of the Recipient, but may not be exercised after one year
from the date of such Disability or death or the expiration of the stated term of the
Option, whichever period is shorter. In the event of termination of employment by reason of
death or Disability, if an Incentive Stock Option is exercised after the expiration of the
exercise periods that apply for purposes of Section 422 of the Code, the Option will
thereafter be treated as a Non-Qualified Option. All Options that are not vested at the
time of termination shall terminate at such time.

     (i) Other Termination. Unless the Option Agreement provides otherwise or the
Committee otherwise determines:

     (i) if a Recipient’s employment by, or service with, the Company or any
Subsidiary or Parent Corporation terminates for any reason other than death,
Disability or as provided in clause (ii) below, the Option shall immediately
terminate;

     (ii) if the Company or any Subsidiary or Parent Corporation terminates the
Recipient’s employment or service without Cause, the Option may thereafter be
exercised to the extent it was exercisable at the time of such termination for three
months from the date of such termination or the expiration of the stated period of
the Option, whichever period is shorter; and

     (iii) in either of (i) or (ii) above, all Options that are not vested at the
time of termination shall terminate at such time.

SECTION 6. Stock Appreciation Rights.

     6.1 Grant. An Award of Stock Appreciation Rights may be granted to a Recipient either
alone or in conjunction with all or part of any Option granted under the Plan. In the case of a
Non-Qualified Option, such rights may be granted either at or after the time of the grant of such
Option. In the case of an Award in conjunction with an Incentive Stock Option, such Award may be
granted only at the time of the grant of the Option.

     6.2  Stock Appreciation Right Exercise Price. The exercise price per share under a
Stock Appreciation Right shall not be less than 100% of the Fair Market Value of the Stock on the
date of grant of such right. In the event the Committee does not fix the exercise price of the
Stock Appreciation Right, the exercise price shall be 100% of Fair Market Value on the date of
grant; provided, however, that the exercise price per share of a Stock Appreciation Right granted
in

12

 

connection with an Option shall be equal to the exercise price per share of Stock under such
Option so long as it is granted on the same date as such Option.

     6.3 Exercise. The Recipient may exercise a Stock Appreciation Right by surrendering
the applicable portion of the Award. Upon such exercise and surrender, the Recipient shall be
entitled to receive an amount determined in the manner described in Section 6.4(b). If the Award
of a Stock Appreciation Right is in connection with an Option, that portion of the Option
representing the Stock Appreciation Rights shall be surrendered upon exercise of the right.
Options that have been so surrendered, in whole or in part, shall no longer be exercisable to the
extent the related Stock Appreciation Rights have been exercised.

     6.4 Terms and Conditions. Stock Appreciation Rights shall be subject to such terms
and conditions, not inconsistent with the provisions of the Plan, as shall be determined from time
to time by the Committee, including the following:

     (a) Award Related to Stock Options. Stock Appreciation Rights granted in
connection with an Option shall be exercisable only at such time or times and to the extent
that the Options to which they relate shall be exercisable in accordance with the provisions
of Section 5 and this Section 6 of the Plan. A Stock Appreciation Right or applicable
portion thereof granted in connection with an Option shall terminate and no longer be
exercisable upon the termination or exercise of the related Option, except that a Stock
Appreciation Right granted with respect to less than the full number of shares covered by a
related Option shall not be reduced until the exercise or termination of the related Option
exceeds the number of shares not covered by the Stock Appreciation Right.

     (b) Payment Upon Exercise. Upon the exercise of a Stock Appreciation Right,
the Recipient shall be entitled to receive an amount in cash or shares of Stock equal in
value to the excess of the Fair Market Value of one share of Stock on the date of exercise
of the Award over the exercise price per share of the Stock Appreciation Right, multiplied
by the number of shares in respect of which the Stock Appreciation Right shall have been
exercised, with the Committee having the right to determine the form of payment.

     (c) Transferability. Except as provided in the next sentence, Stock
Appreciation Rights shall not be transferable except pursuant to the laws of descent upon
death. Stock Appreciation Rights granted in connection with an Option shall be transferable
only when and to the extent that the underlying Option would be transferable under Section
5.4(g) of the Plan.

     (d) Incentive Stock Option Limitation. A Stock Appreciation Right granted in
connection with an Incentive Stock Option may be exercised only if and when the market price
of the Stock subject to the Incentive Stock Option exceeds the exercise price of such
Option.

     (e) Limitation under Section 162(m) of the Code. At such time as any Stock
Appreciation Right under the Plan granted by the Committee is subject to the limitations

13

 

under Section 162(m) of the Code, no Recipient shall receive grants of Stock
Appreciation Rights and Options under the Plan that exceed an aggregate of 1,000,000 shares
of Stock during any fiscal year of the Company.

SECTION 7. Restricted Stock and Restricted Stock Unit Awards.

     7.1 Grant. An Award of Restricted Stock or Restricted Stock Units may be granted
either alone or in addition to other Awards granted under the Plan. The Committee shall determine
to whom Restricted Stock or Restricted Stock Units will be granted, the number of shares of such
Stock or units to be awarded, the times or other conditions within which an Award may be subject to
forfeiture, and all other conditions of the Award in addition to those contained in Section 7.4.
The Committee may also grant Restricted Stock or Restricted Stock Units in which the restrictions
lapse upon the attainment of specified performance goals over a specified performance period. The
provisions of Restricted Stock or Restricted Stock Unit Awards need not be the same with respect to
each Recipient.

     7.2 Award Agreement. The Recipient of an Award of shares of Restricted Stock or
Restricted Stock Units shall not have any rights with respect to such Award, unless and until such
Recipient has executed an Agreement evidencing the Award and has delivered a fully executed copy
thereof to the Company, and has otherwise complied with the then applicable terms and conditions.

     7.3 Restricted Stock Award Certificate. Each Recipient of a Restricted Stock Award
shall be issued a stock certificate in respect of shares of Restricted Stock awarded under the
Plan. Such certificate shall be registered in the name of the Recipient, and shall bear an
appropriate legend referring to the terms, conditions, and restrictions applicable to the Award,
substantially in the following form:

     “The transferability of this certificate and the shares of Stock represented
hereby are subject to the terms and conditions (including forfeiture) of the US
BioEnergy Corporation 2006 Stock Incentive Plan and an Agreement entered into
between the registered owner and the Company. Copies of such Plan and Agreement are
on file in the offices of the Secretary of the Company.”

The Committee shall require that the stock certificates evidencing such shares be held in custody
by the Company until the restrictions thereon shall have lapsed, and that, as a condition of any
Restricted Stock Award, the Recipient shall have delivered a stock power, endorsed in blank,
relating to the Stock covered by such Award.

     7.4 Restrictions and Conditions on Restricted Stock Awards. The shares of Restricted
Stock awarded pursuant to the Plan shall be subject to the following restrictions and conditions:

     (a) Restriction Period. Subject to the provisions of the Plan and the Award
Agreement, during a period set by the Committee commencing with the date of such Award
Agreement (the “Restriction Period”), the Recipient shall not be permitted to sell,
transfer, pledge or assign shares of Restricted Stock awarded under the Plan. Within these
limits, the Committee may provide for the lapse of such restrictions in installments where
deemed appropriate.

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     (b) Rights as Shareholder. Except as provided in Section 7.4(a) and (c) or as
otherwise provided in an Award Agreement, the Recipient shall have, with respect to the
shares of Restricted Stock, all of the rights of a shareholder of the Company, including the
right to vote the shares and the right to receive any cash dividends. The Committee, in its
sole discretion or as otherwise required by application of Section 409A of the Code, may
require the payment of cash dividends to be deferred and, if the Committee so determines,
reinvested in additional shares of Restricted Stock (to the extent shares are available
under Section 3.1). Certificates for shares of unrestricted Stock shall be delivered to the
Recipient promptly after, and only after, the period of forfeiture shall have expired
without forfeiture in respect of such shares of Restricted Stock.

     (c) Performance Restrictions. Notwithstanding Section 7.4(b) above, any Award
of Restricted Stock based on the achievement of performance goals shall not be considered
outstanding for any purpose, and no dividends, voting or other rights of a shareholder shall
attach to such shares until such time as the performance goals have been satisfied and the
shares are issued to the Recipient without restriction.

     (d) Forfeiture; Waiver. Except to the extent provided in an Award Agreement,
upon termination of employment for any reason during the Restriction Period, all shares
still subject to restriction shall be forfeited by the Recipient. The Committee may, in its
sole discretion, when it finds that a waiver would be in the best interest of the Company,
waive in whole or in part any or all remaining restrictions with respect to the Recipient’s
shares of Restricted Stock.

     (e) Transferability. Subject to the provisions of the Plan and an Award
Agreement, Restricted Stock Awards may not be sold, assigned, transferred, pledged or
otherwise encumbered during the Restriction Period.

     7.5 Terms and Conditions of Restricted Stock Unit Awards. The shares of Restricted
Stock awarded pursuant to the Plan shall be subject to the following restrictions and conditions:

          (a) Vesting. At the time of the grant of Restricted Stock Units, the Committee may
impose such restrictions or conditions to the vesting of such Restricted Stock Units as it, in its
sole discretion, deems appropriate, to be contained in an Award Agreement. The Committee may
divide such Restricted Stock Units into classes and assign different vesting conditions for each
class. Provided that all conditions to the vesting of a Restricted Stock Unit are satisfied, and
except as provided in Section 7.5(c), upon the satisfaction of all vesting conditions with respect
to a Restricted Stock Unit, such Restricted Stock Unit shall vest. The provisions of the awards of
Restricted Stock Units need not be the same with respect to each Recipient.

          (b) Shares Upon Vesting. Upon the vesting of Restricted Stock Units, the Recipient
shall be entitled to receive, within 30 days following the date on which such Restricted Stock
Units vest, one share of Stock for each Restricted Stock Unit that so vests.

          (c) Termination of Employment. The rights of Recipients granted a Restricted Stock
Unit upon termination of employment with or service as a director of the Company or any

15

 

Subsidiary or Affiliate for any reason before the Restricted Stock Unit vests shall be set
forth in the Award Agreement governing such Award.

SECTION 8. Deferred Stock Awards.

     8.1 Grant. Deferred Stock may be awarded either alone or in addition to other Awards
granted under the Plan. The Committee shall determine the duration of the period (the “Deferral
Period”) during which, and the conditions under which, receipt of the Stock will be deferred, and
the other terms and conditions of the Award consistent with the terms of the Plan, in addition to
those contained in Section 8.2. The Committee may also condition the receipt of Deferred Stock
upon the attainment of specified performance goals. The provisions of Deferred Stock Awards need
not be the same with respect to each Recipient. Each Award shall be confirmed by, and subject to
the terms of, a Deferred Stock Agreement executed by the Company and the Recipient.

     8.2 Terms and Conditions. The shares of Deferred Stock awarded pursuant to the Plan
shall be subject to the following terms and conditions:

     (a) Transferability. Subject to the provisions of the Plan and the Award
Agreement, Deferred Stock awards may not be sold, assigned, transferred, pledged or
otherwise encumbered during the Deferral Period. At the expiration of the Deferral Period,
share certificates shall be delivered to the Recipient, or his legal representative, in a
number equal to the shares covered by the Deferred Stock Award.

     (b) Rights as Shareholder. An Award of Deferred Stock shall not be considered
outstanding for any purpose, and no dividends, voting or other rights of a shareholder shall
attach to such shares until such time as the Deferral Period has ended and the shares are
issued to the Recipient.

     (c) Forfeiture; Waiver. Except as provided in the Award Agreement, upon
termination of employment for any reason during the Deferral Period for a given award, the
Recipient shall forfeit the Deferred Stock in question. To the extent permitted by Section
409A, the Committee may, in its sole discretion, when it finds that a waiver would be in the
best interest of the Company, waive in whole or in part any or all of the remaining deferral
limitations imposed hereunder with respect to any or all of the Recipient’s Deferred Stock.

SECTION 9. Performance Stock, Director Stock and Other Awards

     9.1 Grant of Performance Stock. An Award of Performance Stock may be granted either
alone or in addition to other Awards granted under the Plan. The Committee shall determine to whom
Performance Stock will be granted, the number of shares of Stock to be awarded, the times of grant
or other conditions, including attainment of specified performance goals over a specified
performance period upon which an Award will no longer be subject to forfeiture, and all other
conditions of the Award consistent with the terms of the Plan. The Committee may also grant
unrestricted Stock in connection with the performance of services for or on behalf of the Company,
which may include the grant of unrestricted Stock to members of the Board of

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Directors. The provisions of Performance Stock Awards need not be the same with respect to
each Recipient.

     9.2 Director Stock. Commencing as of the Effective Date, and unless otherwise
determined by the Committee, any director of the Company who is entitled to an annual retainer fee
from the Company will be permitted to make a written election, prior to the commencement of the
year for which the fee is payable, to reduce the cash portion of such annual retainer fee by a
specified percentage, up to 100%, and have such amount paid instead in the form of an Award of
unrestricted Stock under the Plan, provided that cash will be paid in lieu of fractional shares.
The Committee shall, from time to time, establish such rules and procedures to implement the
foregoing, including rules and procedures relating to the form used to make the election and the
time by which the election form must be properly submitted. No director will be permitted to make,
change or revoke any election for the applicable year following the deadline for submitting the
election form.

     9.3 Grant of Other Awards. Other forms of Awards (“Other Awards”) valued in whole or
in part by reference to, or otherwise based on, shares of Stock, dividends with respect thereto or
other units or measures may be granted either alone or in addition to other Awards under the Plan.
Subject to the provisions of the Plan, the Committee shall have sole and complete authority to
determine the persons to whom and the time or times at which such Other Awards shall be granted,
the number of shares of Stock to be granted pursuant to such Other Awards and all other terms and
conditions of such Other Awards.

SECTION 10. Change in Control.

     10.1 Automatic Acceleration. Upon the occurrence of a Change in Control, except as
otherwise provided in an Agreement, all outstanding Awards granted to a Recipient that have not
theretofore vested shall immediately vest and all restrictions on such Awards shall immediately
lapse, and each Option and Stock Appreciation Right granted to a Recipient and outstanding at such
time shall become fully and immediately exercisable. Except as otherwise provided in an Agreement,
each outstanding Option and Stock Appreciation Right granted pursuant to the Plan that shall not
have been exercised immediately prior to the Change in Control shall be cancelled as of the Change
in Control, subject to any payment obligations of the Company provided in Section 11.

     10.2 Limitation on Change in Control Payments. Notwithstanding anything in Section
10.1 or Section 11 to the contrary, if, with respect to a Recipient, the acceleration of the
exercisability or vesting of an Award or the payment of cash in exchange for all or part of an
Award as provided in Section 10.1 or Section 11 (which acceleration or payment could be deemed a
“parachute payment” within the meaning of Section 280G(b)(2) of the Code), together with any other
payments which such Recipient has the right to receive would constitute an “excess parachute
payment” (within the meaning of Section 280G(b)(1) of the Code), then, unless otherwise provided in
the applicable Award Agreement, such acceleration of exercisability or vesting and payments
pursuant to the Plan shall be reduced to the largest amount as, in the sole judgment of the
Committee, will result in no portion of such payments being subject to the excise tax imposed by
Section 4999 of the Code.

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SECTION 11. Additional Change in Control Provisions.

     11.1 Effect on Award. In addition to the provisions of Section 10, upon the
occurrence of a Change in Control, the Committee may, but shall not be obligated to:

     (a) Substitution of Award. Make appropriate provision for the protection of
outstanding Awards granted under the Plan by the substitution of other awards in lieu of
such Awards, which other awards are designed to preserve the value of the Awards granted
under the Plan; or

     (b) Cancellation of Options. With respect to any Option, declare, at least
twenty days prior to the Change in Control, and provide written notice to each Recipient of
the declaration, that each outstanding Option, whether or not then exercisable, shall be
cancelled at the time of, or immediately prior to the occurrence of, the Change in Control
(unless it shall have been exercised prior to the occurrence of the Change in Control); or

     (c) Cash Payment. Cause payment to be made, within twenty days after the
Change in Control, in exchange for each cancelled Award to each Recipient of an Award that
is cancelled, of cash equal to the Fair Market Value for each share of Stock covered by the
cancelled Award, except that with respect to any cancelled Option, cash equal to the amount,
(if any), by which the per Share transaction consideration (taking into account such
considerations as the Committee deems appropriate in determining this value) exceeds the
exercise price per share of Stock covered by such Option.

     11.2 Notwithstanding the foregoing, no Recipient of an Award shall be entitled to the payment
provided in this Section 11 if such Award shall have expired or otherwise been cancelled pursuant
to the terms of the Plan or applicable Agreement.

SECTION 12. Substitute Awards.

     12.1 Purpose. Awards may be granted under the Plan from time to time in substitution
for Awards held by employees of other corporations who are about to become employees of the
Company, or any Parent Corporation or Subsidiary thereof, or whose employer is about to become a
Subsidiary of the Company, as the result of a merger or consolidation of the Company or its
Subsidiary with another corporation, the acquisition by the Company or its Subsidiary of all or
substantially all the assets of another corporation, the acquisition by the Company or its
Subsidiary of at least 50% of the issued and outstanding stock of another corporation or such other
similar corporate transaction as determined by the Committee, in its sole discretion.

     12.2 Terms and Conditions. To the extent permitted by applicable law, the terms and
conditions of the substitute Award so granted may vary from the terms and conditions set forth in
the Plan to such extent as the Committee at the time of the grant may deem appropriate to conform,
in whole or in part, to the provisions of the stock awards in substitution for which they are
granted, but with respect to incentive stock options (as defined in Section 422 of the Code),
unless otherwise determined by the Committee, no such variation shall be permitted that affects the
status of any such substitute Option as an Incentive Stock Option.

SECTION 13. General Provisions.

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     13.1 Compliance With Laws. No Stock will be issued pursuant to the Plan unless in
compliance with applicable legal requirements, including without limitation, those relating to
securities laws and stock exchange listing requirements. The Committee may require each Recipient
receiving Stock pursuant to an Award under the Plan to represent to and agree with the Company in
writing that such person is acquiring the Stock without a view to distribution thereof.

     13.2 Stop Transfer Order. All certificates for Stock delivered under the Plan shall
be subject to such stop transfer orders and other restrictions as the Committee may deem advisable
under the rules, regulations, and other requirements of the Securities and Exchange Commission, any
stock exchange upon which the Stock is then listed, and any applicable federal or state securities
laws, and the Committee may cause a legend or legends to be put on any such certificates to make
appropriate reference to such restrictions. The issuance of Stock may be affected on a
non-certificated basis to the extent not prohibited by applicable law or the applicable rules of
any stock exchange upon which the Stock is then listed.

     13.3 No Rights to Employment; No Rights as a Shareholder. The adoption of the Plan
shall not confer upon any employee or Consultant of the Company, any Parent Corporation, or any
Subsidiary any right to continued employment or contract with the Company, any Parent Corporation,
or any Subsidiary, as the case may be, nor shall it interfere in any way with the right of the
Company, any Parent Corporation, or any Subsidiary to terminate the employment of any of its
employees or Consultants at any time.

     13.4 Restrictions on Stock Transfers. As a further condition to the grant of any
Award or the issuance of Stock to the Recipient, the Recipient agrees to the following:

     (a) Underwriter Lockup Agreement. In the event the Company advises the
Recipient that it plans an underwritten public offering of its Stock in compliance with the
Securities Act of 1933, as amended (or the Committee determines that this Section 13.4
should otherwise be applicable in connection with such offering), and the Company or the
underwriter(s) seek to impose restrictions under which certain shareholders may not sell or
contract to sell or grant any option to buy or otherwise dispose of part or all of their
stock purchase rights of the underlying Stock, the Recipient will not, for a period not to
exceed 180 days from the prospectus, unless otherwise determined by the Committee, sell or
contract to sell or grant an option to buy or otherwise dispose of any Award granted to
Recipient pursuant to the Plan or any of the underlying Stock without the prior written
consent of the Company and the underwriter(s) or its representative(s).

     (b) Blue Sky Requirements. In the event the Company makes any public offering
of its securities and determines in its sole discretion that it is necessary to reduce the
number of issued but unexercised stock purchase rights so as to comply with any state’s
securities or Blue Sky law limitations with respect thereto, the Board shall have the right:

     (i) to accelerate the vesting and payment of any Award and the exercisability
of any Option and the date on which such Option must be exercised, provided that the
Company gives the Recipient prior written notice of such acceleration, and

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     (ii) to cancel any Option or portion of any Option thereof which the Recipient
does not exercise prior to or contemporaneously with such public offering.

     (c) Legend. The Company may insert a legend on any Stock certificate issued
pursuant to an Award under the Plan to assure compliance with this Section 13.4.

     13.5 Effect of Transfer/Leave of Absence. For purposes of any Incentive Stock Option,
the following events shall not be deemed a termination of employment:

     (a) Transfer. A transfer of an employee from the Company to a Parent
Corporation or a Subsidiary, or a transfer of an employee from a Parent Corporation or a
Subsidiary to the Company or any other Parent Corporation or Subsidiary;

     (b) Leave Less Than 90 Days. A leave of absence, approved in writing by the
Company, for sickness or for any other purpose, if the period of such leave does not exceed
ninety (90) days (or such longer period as the Committee may approve, in its sole
discretion); and

     (c) Leave More Than 90 Days. A leave of absence in excess of ninety (90) days,
approved in writing by the Company, but only if the employee’s right to reemployment is
guaranteed either by a statute or by contract, and provided that, in the case of any leave
of absence, the employee returns to work within 30 days after the end of such leave.

     (d) Military Leave. A military leave in which the employee’s right to
reemployment is guaranteed under the provisions of the Uniform Services Employment and
Reemployment Rights Act (USERRA), and regulations promulgated thereunder.

     13.6 Tax Withholding. Each Recipient shall, no later than the date as of which any
part of the value of an Award first becomes includable as compensation in the income of the
Recipient for income tax purposes, pay to the Company, or make arrangements satisfactory to the
Committee regarding payment of, any federal, state, or local taxes of any kind required by law to
be withheld with respect to the award. The obligations of the Company under the Plan shall be
conditional on such payment or arrangements and the Company, any Parent Corporation, and any
Subsidiary shall, to the extent permitted by law, have the right to deduct any such taxes from any
payment of any kind otherwise due to the Recipient. If the terms of an Award so permit, a
Recipient may elect by written notice to the Company to satisfy part or all of the withholding tax
requirements associated with the award by:

     (a) Retention Stock. Authorizing the Company to retain from the number of
shares of Stock that would otherwise be deliverable to the Recipient, or

     (b) Delivery of Held Stock. Delivering to the Company from Stock already owned
by the Recipient, that number of shares having an aggregate Fair Market Value equal to part
or all of the tax payable by the Recipient under this Section 13.6, and in the event shares
of Stock are withheld, the amount withheld shall not exceed the minimum required federal,
state and FICA withholding amount.

20

 

Any such election shall be in accordance with, and subject to, applicable tax and securities laws,
regulations and rulings, accounting rules, regulations and requirements and any other rules or
regulations established by the Committee.

SECTION 14. Amendments and Termination.

     The Board may amend, alter, or discontinue the Plan, but no amendment, alteration, or
discontinuation shall be made: which would impair the rights of a Recipient under an Award
theretofore granted and vested, without the Recipient’s consent. In addition, unless the Board
determines otherwise, the Board shall obtain approval of the Company’s shareholders for any
amendment that would require such approval in order to satisfy the requirements of Section 162(m)
of the Code, Section 422 of the Code, stock exchange rules or other applicable law. The Committee
may amend the terms of any Award theretofore granted, prospectively or retroactively; however,
subject to Sections 3, 10 and 11 of the Plan, no such amendment shall impair the rights of any
Recipient without his or her consent. Adjustments made by the Committee pursuant to Section 3
(relating to adjustments of Stock) and Section 11 shall not be subject to the foregoing limitations
of this Section 14. Notwithstanding the foregoing provisions of this Section 14, (a) neither the
Plan nor any outstanding Option or Stock Appreciation Right shall be amended to decrease the
exercise price of such Award unless first approved by the requisite vote of shareholders, and (b)
neither the Plan nor any outstanding Agreement shall be amended in any way that could cause an
outstanding Award that is not subject to the tax described in Section 409A of the Code to be
subject to such tax.

SECTION 15. Governing Law.

     To the extent that federal laws do not otherwise control, the Plan and all determinations made
and actions taken under the Plan shall be governed by the laws of the State of South Dakota,
without regard to the conflicts of law provisions thereof, and construed accordingly.

SECTION 16. Effective Date and Term of Plan.

The Plan
was adopted by the Board on November 17, 2006 (the “Effective Date”), subject to approval
by the shareholders of the Company within 12 months before or after the adoption of the Plan by the
Board. Any Incentive Stock Option granted after adoption of the Plan by the Board will be treated
as a Non-Qualified Option if shareholder approval is not obtained within such 12-month period. The
Plan shall be in effect until November 17, 2016, unless earlier terminated by the Board in
accordance with Section 14 hereof. No future Awards may be granted after termination of the Plan,
but previously granted Awards shall remain outstanding in accordance with their applicable terms
and conditions and the terms and conditions of the
Plan.

SECTION 17. Unfunded Status of Plan.

The Plan is intended to constitute an “unfunded” plan for incentive compensation. With respect to
any payments not yet made to a Recipient by the Company, nothing contained herein shall give any
such Recipient any rights that are greater than those of a general creditor of the Company.

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