Document:

exv4w7

Exhibit 4.7

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES
ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT
TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR
HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES LAW OR, IN
THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER OF THESE SECURITIES,
SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION.

WARRANT TO PURCHASE STOCK

	 	 	 

	Company:

	 	KiOR Inc., a Delaware corporation
	 
	 	 
	Number of Shares:

	 	the whole number derived from the quotient of (a) $50,000, divided by (b) the Warrant Price.
	 
	 	 
	Class of Stock:

	 	The class or series of the Company’s preferred stock (the “Next Equity Securities”) issued in connection with
the conversion of that certain Convertible Promissory Note dated August 5, 2009 (the “Note”) issued by the
Company to Kholsa Ventures III, LP upon a Qualified Financing (as defined in the Note) occurring after the
date hereof (the “Next Equity Financing”) or, if such Next Equity Financing does not occur prior to March 25,
2012, the Company’s Series A-1 Preferred Stock, par value $0.001 per share (“Series A-1 Preferred Stock”).
	 
	 	 
	Warrant Price:

	 	If the Class of Stock is Next Equity Securities, the price per share of the Next Equity Securities issued to
Khosla Ventures III, L.P.; or if the Class of Stock is Series A-1 Preferred Stock, $3.89 per share, as
adjusted pursuant to Article 2 hereof
	 
	 	 
	Issue Date:

	 	March 25, 2010
	 
	 	 
	Expiration Date:

	 	The longer of (i) the 10th anniversary after the Issue Date, or (ii)
the 5th anniversary of Company’s initial public offering of common
stock.
	 
	 	 
	Credit Facility:

	 	This Warrant is issued in connection with the Equipment Loan as defined and referenced in that certain Loan
and Security Agreement between Company and Silicon Valley Bank dated of even date herewith

     THIS WARRANT CERTIFIES THAT, for good and valuable consideration, SILICON VALLEY BANK (Silicon
Valley Bank, together with any registered holder from time to time of this Warrant or any holder of
the shares issuable or issued upon exercise of this Warrant, the “Holder”) is entitled to purchase
the number of fully paid and nonassessable shares of the Class of Stock (the “Shares”) of the
Company at the Warrant Price, all as set forth above and as adjusted pursuant to Article 2 of this

 

 

Warrant, subject to the provisions and upon the terms and conditions set forth in this Warrant.

ARTICLE 1. EXERCISE.

          1.1 Method of Exercise. Holder may exercise this Warrant by delivering a duly
executed Notice of Exercise in substantially the form attached as Appendix 1 to the principal
office of the Company. Unless Holder is exercising the conversion right set forth in Article 1.2,
Holder shall also deliver to the Company a check, wire transfer (to an account designated by the
Company), or other form of payment acceptable to the Company for the aggregate Warrant Price for
the Shares being purchased.

          1.2 Conversion Right. In lieu of exercising this Warrant as specified in Article 1.1,
Holder may from time to time convert this Warrant, in whole or in part, into a number of Shares
determined by dividing (a) the aggregate fair market value of the Shares or other securities
otherwise issuable upon exercise of this Warrant minus the aggregate Warrant Price of such Shares
by (b) the fair market value of one Share. The fair market value of the Shares shall be determined
pursuant to Article 1.3.

          1.3 Fair Market Value. If the Company’s common stock is traded in a public market and
the Shares are common stock, the fair market value of each Share shall be the closing price of a
Share reported for the business day immediately before Holder delivers its Notice of Exercise to
the Company (or in the instance where the Warrant is exercised immediately prior to the
effectiveness of the Company’s initial public offering, the “price to public” per share price
specified in the final prospectus relating to such offering). If the Company’s common stock is
traded in a public market and the Shares are preferred stock, the fair market value of a Share
shall be the closing price of a share of the Company’s common stock reported for the business day
immediately before Holder delivers its Notice of Exercise to the Company (or, in the instance where
the Warrant is exercised immediately prior to the effectiveness of the Company’s initial public
offering, the initial “price to public” per share price specified in the final prospectus relating
to such offering), in both cases, multiplied by the number of shares of the Company’s common stock
into which the Shares are convertible. If the Company’s common stock is not traded in a public
market, the Board of Directors of the Company shall determine fair market value in its reasonable
good faith judgment.

          1.4 Delivery of Certificate and New Warrant. Promptly after Holder exercises or
converts this Warrant and, if applicable, the Company receives payment of the aggregate Warrant
Price, the Company shall deliver to Holder certificates for the Shares acquired and, if this
Warrant has not been fully exercised or converted and has not expired, a new Warrant representing
the Shares not so acquired.

          1.5 Replacement of Warrants. On receipt of evidence reasonably satisfactory to the
Company of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss,
theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and
amount to the Company or, in the case of mutilation on surrender and cancellation of this Warrant,
the Company shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor.

          1.6 Treatment of Warrant Upon Acquisition of Company.

 

 

               1.6.1 “Acquisition”. For the purpose of this Warrant, “Acquisition” means any sale,
license, or other disposition of all or substantially all of the assets of the Company, or any
reorganization, consolidation, or merger of the Company where the holders of the Company’s
securities before the transaction beneficially own less than 50% of the outstanding voting
securities of the surviving entity after the transaction.

               1.6.2 Treatment of Warrant at Acquisition.

A) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition that
is not an asset sale and in which the sole consideration is cash, either (1) Holder shall exercise
its conversion or purchase right under this Warrant and such exercise will be deemed effective
immediately prior to the consummation of such Acquisition or (2) if Holder elects not to exercise
the Warrant, this Warrant will expire upon the consummation of such Acquisition. The Company shall
provide Holder with written notice of its request relating to the foregoing (together with such
reasonable information as Holder may request in connection with such contemplated Acquisition
giving rise to such notice), which is to be delivered to Holder not less than ten (10) days prior
to the closing of the proposed Acquisition.

B) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition that
is an “arms length” sale of all or substantially all of the Company’s assets (and only its assets)
to a third party that is not an Affiliate (as defined below) of the Company (a “True Asset Sale”),
either (1) Holder shall exercise its conversion or purchase right under this Warrant and such
exercise will be deemed effective immediately prior to the consummation of such Acquisition or (2)
if Holder elects not to exercise the Warrant, this Warrant will continue until the Expiration Date
if the Company continues as a going concern following the closing of any such True Asset Sale. The
Company shall provide Holder with written notice of its request relating to the foregoing (together
with such reasonable information as Holder may request in connection with such contemplated
Acquisition giving rise to such notice), which is to be delivered to Holder not less than ten (10)
days prior to the closing of the proposed Acquisition.

C) Upon the written request of the Company, Holder agrees that, in the event of a stock for stock
Acquisition of the Company by a publicly traded acquirer if, on the record date of the Acquisition,
the fair market value of each of the Shares (or other securities issuable upon exercise of the
Warrant) is equal to or greater than two (2) times the Warrant Price, the Company may require the
Warrant to be deemed automatically exercised and the Holder shall participate in the Acquisition as
a holder of the Shares (or other securities issuable upon exercise of the Warrant) on the same
terms as the other holders of the same class of securities of the Company.

D) Upon the closing of any Acquisition other than those particularly described in subsections (A)
and (B) above, the successor entity shall assume the obligations of this Warrant, and this Warrant
shall be exercisable for the same securities, cash, and property as would be payable for the Shares
issuable upon exercise of the unexercised portion of this Warrant as if such Shares were
outstanding on the record date for the Acquisition and subsequent closing. The Warrant Price
and/or number of Shares shall be adjusted accordingly.

 

 

As used herein “Affiliate” shall mean any person or entity that owns or controls directly
or indirectly ten (10) percent or more of the stock of Company, any person or entity that controls
or is controlled by or is under common control with such persons or entities, and each of such
person’s or entity’s officers, directors, joint venturers or partners, as applicable.

ARTICLE 2. ADJUSTMENTS TO THE SHARES.

          2.1 Stock Dividends, Splits, Etc. If the Company declares or pays a dividend on the
Shares payable in common stock, or other securities, then upon exercise of this Warrant, for each
Share acquired, Holder shall receive, without cost to Holder, the total number and kind of
securities to which Holder would have been entitled had Holder owned the Shares of record as of the
date the dividend occurred. If the Company subdivides the Shares by reclassification or otherwise
into a greater number of shares or takes any other action which increase the amount of stock into
which the Shares are convertible, the number of shares purchasable hereunder shall be
proportionately increased and the Warrant Price shall be proportionately decreased. If the
outstanding shares are combined or consolidated, by reclassification or otherwise, into a lesser
number of shares, the Warrant Price shall be proportionately increased and the number of Shares
shall be proportionately decreased.

          2.2 Reclassification, Exchange, Combinations or Substitution. Upon any
reclassification, exchange, substitution, or other event that results in a change of the number
and/or class of the securities issuable upon exercise or conversion of this Warrant, Holder shall
be entitled to receive, upon exercise or conversion of this Warrant, the number and kind of
securities and property that Holder would have received for the Shares if this Warrant had been
exercised immediately before such reclassification, exchange, substitution, or other event. Such
an event shall include any automatic conversion of the outstanding or issuable securities of the
Company of the same class or series as the Shares to common stock pursuant to the terms of the
Company’s Certificate of Incorporation upon the closing of a registered public offering of the
Company’s common stock. The Company or its successor shall promptly issue to Holder an amendment
to this Warrant setting forth the number and kind of such new securities or other property issuable
upon exercise or conversion of this Warrant as a result of such reclassification, exchange,
substitution or other event that results in a change of the number and/or class of securities
issuable upon exercise or conversion of this Warrant. The amendment to this Warrant shall provide
for adjustments which shall be as nearly equivalent as may be practicable to the adjustments
provided for in this Article 2 including, without limitation, adjustments to the Warrant Price and
to the number of securities or property issuable upon exercise of the new Warrant. The provisions
of this Article 2.2 shall similarly apply to successive reclassifications, exchanges,
substitutions, or other events.

          2.3 Adjustments for Diluting Issuances. The Warrant Price and the number of Shares
issuable upon exercise of this Warrant or, if the Shares are preferred stock, the number of shares
of common stock issuable upon conversion of the Shares, shall be subject to adjustment, from time
to time in the manner set forth in the Company’s Certificate of Incorporation as if the Shares
were issued and outstanding on and as of the date of any such required adjustment. The provisions
set forth for the Shares in the Company’s Certificate of Incorporation relating to the above in
effect as of the Issue Date may not be amended, modified or waived, without the prior written

 

 

consent of Holder unless such amendment, modification or waiver affects the rights associated
with the Shares in the same manner as such amendment, modification or waiver affects the rights
associated with all other shares of the same series and class as the Shares granted to Holder.

          2.4 No Impairment. The Company shall not, by amendment of its Certificate of
Incorporation or through a reorganization, transfer of assets, consolidation, merger, dissolution,
issue, or sale of securities or any other voluntary action, avoid or seek to avoid the observance
or performance of any of the terms to be observed or performed under this Warrant by the Company,
but shall at all times in good faith assist in carrying out of all the provisions of this Article 2
and in taking all such action as may be necessary or appropriate to protect Holder’s rights under
this Article against impairment.

          2.5 Fractional Shares. No fractional Shares shall be issuable upon exercise or
conversion of this Warrant and the number of Shares to be issued shall be rounded down to the
nearest whole Share. If a fractional share interest arises upon any exercise or conversion of the
Warrant, the Company shall eliminate such fractional share interest by paying Holder the amount
computed by multiplying the fractional interest by the fair market value of a full Share.

          2.6 Certificate as to Adjustments. Upon each adjustment of the Warrant Price, the
Company shall promptly notify Holder in writing, and, at the Company’s expense, promptly compute
such adjustment, and furnish Holder with a certificate of its Chief Financial Officer setting forth
such adjustment and the facts upon which such adjustment is based. The Company shall, upon written
request, furnish Holder a certificate setting forth the Warrant Price in effect upon the date
thereof and the series of adjustments leading to such Warrant Price.

ARTICLE 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY.

          3.1 Representations and Warranties. The Company represents and warrants to Holder as
follows:

               (a) The initial Warrant Price (for purposes of clarity, for the Series A-1 Preferred Stock of
the Company) referenced on the first page of this Warrant is not greater than the price per share
at which the Series A-1 Preferred Stock of the Company was last issued in an arms-length
transaction in which at least $500,000 of the Series A-1 Preferred Stock was sold.

               (b) All Shares which may be issued upon the exercise of the purchase right represented by this
Warrant, and all securities, if any, issuable upon conversion of the Shares, shall, upon issuance,
be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and
encumbrances except for restrictions on transfer provided for herein or under applicable federal
and state securities laws.

               (c) The Company further covenants and agrees that during the period within which the rights
represented by this Warrant may be exercised, the Company will at all times have authorized and
reserved for the purpose of issue or transfer upon exercise of the subscription rights evidenced by
this Warrant, a sufficient number of Shares of authorized but unissued stock, or other securities
and property,

 

 

when and as required to provide for the exercise of the rights represented by this Warrant.

               (d) As of the date hereof, the authorized capital stock of the Company consists of (i)
9,200,000 shares of Common Stock, $0.001 par value, of which 1,800,000 shares are issued and
outstanding, (ii) 3,000,000 shares of Series A Preferred Stock, of which 3,000,000 are issued and
outstanding shares, and (iii) 3,200,000 shares of Series A-1 Preferred Stock, of which 2,571,447
are issued and outstanding shares.

          3.2 Notice of Certain Events. If the Company proposes at any time (a) to declare any
dividend or distribution upon any of its stock, whether in cash, property, stock, or other
securities and whether or not a regular cash dividend; (b) to offer for sale any shares of the
Company’s capital stock (or other securities convertible into such capital stock), other than (i)
pursuant to the Company’s stock option or other compensatory plans, (ii) in connection with
commercial credit arrangements or equipment financings, or (iii) in connection with strategic
transactions for purposes other than capital raising; (c) to effect any reclassification or
recapitalization of any of its stock; (d) to merge or consolidate with or into any other
corporation, or sell, lease, license, or convey all or substantially all of its assets, or to
liquidate, dissolve or wind up; or (e) offer holders of registration rights the opportunity to
participate in an underwritten public offering of the Company’s securities for cash, then, in
connection with each such event, the Company shall give Holder: (1) at least 10 days prior written
notice of the date on which a record will be taken for such dividend, distribution, or subscription
rights (and specifying the date on which the holders of common stock will be entitled thereto) or
for determining rights to vote, if any, in respect of the matters referred to in (a) and (b) above;
(2) in the case of the matters referred to in (c) and (d) above at least 10 days prior written
notice of the date when the same will take place (and specifying the date on which the holders of
common stock will be entitled to exchange their common stock for securities or other property
deliverable upon the occurrence of such event); and (3) in the case of the matter referred to in
(e) above, the same notice as is given to the holders of such registration rights. Company agrees
to provide information reasonably requested by Holder necessary to enable Holder to comply with
Holder’s accounting or reporting requirements.

          3.3 Registration Under Securities Act of 1933, as amended. The Company agrees that
the Shares or, if the Shares are convertible into common stock of the Company, such common stock,
shall have certain “piggyback,” registration rights pursuant to and as set forth in the Company’s
Investor Rights Agreement or similar agreement. The provisions set forth in the Company’s
Investors’ Right Agreement or similar agreement relating to the above in effect as of the Issue
Date may not be amended, modified or waived without the prior written consent of Holder unless such
amendment, modification or waiver affects the rights associated with the Shares in the same manner
as such amendment, modification, or waiver affects the rights associated with all other shares of
the same series and class as the Shares granted to Holder.

          3.4 No Shareholder Rights. Except as provided in this Warrant, Holder will not have
any rights as a shareholder of the Company until the exercise of this Warrant.

 

 

ARTICLE 4. REPRESENTATIONS, WARRANTIES OF HOLDER. Holder represents and warrants to the
Company as follows:

          4.1 Purchase for Own Account. This Warrant and the securities to be acquired upon
exercise of this Warrant by Holder will be acquired for investment for Holder’s account, not as a
nominee or agent, and not with a view to the public resale or distribution within the meaning of
the Act. Holder also represents that Holder has not been formed for the specific purpose of
acquiring this Warrant or the Shares.

          4.2 Disclosure of Information. Holder has received or has had full access to all the
information it considers necessary or appropriate to make an informed investment decision with
respect to the acquisition of this Warrant and its underlying securities. Holder further has had
an opportunity to ask questions and receive answers from the Company regarding the terms and
conditions of the offering of this Warrant and its underlying securities and to obtain additional
information (to the extent the Company possessed such information or could acquire it without
unreasonable effort or expense) necessary to verify any information furnished to Holder or to which
Holder has access.

           4.3 Investment Experience. Holder understands that the purchase of this
Warrant and its underlying securities involves substantial risk. Holder has experience as an
investor in securities of companies in the development stage and acknowledges that Holder can bear
the economic risk of such Holder’s investment in this Warrant and its underlying securities and has
such knowledge and experience in financial or business matters that Holder is capable of evaluating
the merits and risks of its investment in this Warrant and its underlying securities and/or has a
preexisting personal or business relationship with the Company and certain of its officers,
directors or controlling persons of a nature and duration that enables Holder to be aware of the
character, business acumen and financial circumstances of such persons.

          4.4 Accredited Investor Status. Holder is an “accredited investor” within the meaning
of Regulation D promulgated under the Act.

          4.5 The Act. Holder understands that this Warrant and the Shares issuable upon
exercise or conversion hereof have not been registered under the Act in reliance upon a specific
exemption therefrom, which exemption depends upon, among other things, the bona fide nature of
Holder’s investment intent as expressed herein. Holder understands that this Warrant and the
Shares issued upon any exercise or conversion hereof must be held indefinitely unless subsequently
registered under the Act and qualified under applicable state securities laws, or unless exemption
from such registration and qualification are otherwise available.

ARTICLE 5. MISCELLANEOUS.

          5.1 Term. This Warrant is exercisable in whole or in part at any time and from time
to time on or before the Expiration Date.

           5.2 Legends. This Warrant and the Shares (and the securities issuable,
directly or indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in
substantially the following form:

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE

 

 

NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR
THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF
ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR
HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE
SECURITIES LAW OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE
SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER,
PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION.

          5.3 Compliance with Securities Laws on Transfer. This Warrant and the Shares issuable
upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion
of the Shares, if any) may not be transferred or assigned in whole or in part without compliance
with applicable federal and state securities laws by the transferor and the transferee (including,
without limitation, the delivery of investment representation letters and legal opinions reasonably
satisfactory to the Company, as reasonably requested by the Company); provided, that, the Company
shall not require Silicon Valley Bank (“Bank”) to provide an opinion of counsel if the transfer is
to Bank’s parent company, SVB Financial Group (formerly Silicon Valley Bancshares), or any other
affiliate of Bank. In addition, the Company shall not require an opinion of counsel if there is no
material question as to the availability of current information as referenced in Rule 144(c), as
determined in the sole discretion of the Company, Holder represents that it has complied with Rule
144(d) and (e) in reasonable detail, the selling broker represents that it has complied with Rule
144(f), and the Company is provided with a copy of Holder’s notice of proposed sale.

          5.4 Transfer Procedure. After receipt by Bank of the executed Warrant, Bank will
transfer all of this Warrant to SVB Financial Group by execution of an Assignment substantially in
the form of Appendix 2. Subject to the provisions of Article 5.3 and upon providing the Company
with written notice, SVB Financial Group and any subsequent Holder may transfer all or part of this
Warrant or the Shares issuable upon exercise of this Warrant (or the Shares issuable directly or
indirectly, upon conversion of the Shares, if any) to any transferee, provided, however, in
connection with any such transfer, SVB Financial Group or any subsequent Holder will give the
Company notice of the portion of the Warrant being transferred with the name, address and taxpayer
identification number of the transferee and Holder will surrender this Warrant to the Company for
reissuance to the transferee(s) (and Holder if applicable). The Company may refuse to transfer
this Warrant or the Shares to any person who directly competes with the Company, unless, in either
case, the stock of the Company is publicly traded.

          5.5 Notices. All notices and other communications from the Company to Holder, or vice
versa, shall be deemed delivered and effective when given personally or mailed by first-class
registered or certified mail, postage prepaid, at such address as may have been furnished to the
Company or Holder, as the case may (or on the first business day after transmission by facsimile)
be, in writing by the Company or such Holder from time to time. Effective upon receipt of the
fully executed Warrant and the initial transfer described in Article 5.4 above, all notices to
Holder shall be addressed as follows until the Company receives notice of a change of address in
connection with a transfer or otherwise:

 

 

SVB Financial Group

Attn: Treasury Department

3003 Tasman Drive, HA 200

Santa Clara, CA 95054

Telephone: 408-654-7400

Facsimile: 408-496-2405

Notice to the Company shall be addressed as follows until Holder receives notice of a change in
address:

KiOR, Inc.

Attn: Fred Cannon, President and CEO

13001 Bay Park Road

Pasadena, Texas 77507

Telephone: 281-694-8700

          5.6 Waiver. This Warrant and any term hereof may be changed, waived, discharged or
terminated only by an instrument in writing signed by the party against which enforcement of such
change, waiver, discharge or termination is sought.

          5.7 Attorneys’ Fees. In the event of any dispute between the parties concerning the
terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to
collect from the other party all costs incurred in such dispute, including reasonable attorneys’
fees.

          5.8 Automatic Conversion upon Expiration. In the event that, upon the Expiration
Date, the fair market value of one Share (or other security issuable upon the exercise hereof) as
determined in accordance with Section 1.3 above is greater than the Warrant Price in effect on such
date, then this Warrant shall automatically be deemed on and as of such date to be converted
pursuant to Section 1.2 above as to all Shares (or such other securities) for which it shall not
previously have been exercised or converted, and the Company shall promptly deliver a certificate
representing the Shares (or such other securities) issued upon such conversion to Holder.

          5.9 Counterparts. This Warrant may be executed in counterparts, all of which together
shall constitute one and the same agreement.

          5.10 Governing Law. This Warrant shall be governed by and construed in accordance
with the laws of the State of California, without giving effect to its principles regarding
conflicts of law.

[Signature page follows.]

 

 

	 	 	 	 	 	 	 

	“COMPANY”	 	Date:	 	March 24, 2010
	 
	 	 	 	 	 	 
	KIOR, INC.,	 	 	 	 
	a Delaware corporation	 	 	 	 
	 
	 	 	 	 	 	 
	By:

	 	/s/ Fred Cannon
	 	By:
	 	/s/ Andre Ditsch
	 

	 	 
	 	 	 	 
	Name:

	 	Fred Cannon
	 	Name:
	 	Andre Ditsch
	 

	 	 
	 	 	 	 
	 

	 	(Print)
	 	 	 	(Print)
	Title:

	 	President and CEO
	 	Title:
	 	Secretary of the Board — KiOR, Inc.
	 
	 	 	 	 	 	 
	“HOLDER”	 	 	 	 
	 
	 	 	 	 	 	 
	SILICON VALLEY BANK	 	 	 	 
	 
	 	 	 	 	 	 
	By:

	 	/s/ Philip A. Wright	 	 	 	 
	 

	 	 	 	 	 	 
	Name:

	 	Philip A. Wright	 	 	 	 
	 

	 	 	 	 	 	 
	 

	 	(Print)	 	 	 	 
	Title:

	 	Relationship Manager	 	 	 	 

 

 

APPENDIX 1

NOTICE OF EXERCISE

     1. Holder elects to purchase ___________ shares of the Common/Series ______ Preferred [strike
one] Stock of __________________ pursuant to the terms of the attached Warrant, and tenders payment
of the purchase price of the shares in full.

          [or]

     1. Holder elects to convert the attached Warrant into Shares/cash [strike one] in the manner
specified in the Warrant. This conversion is exercised for _____________________ of the Shares
covered by the Warrant.

     [Strike paragraph that does not apply.]

     2. Please issue a certificate or certificates representing the shares in the name specified
below:

	 	 	 	 	 

	 

	 	 

	 	 
	 

	 	                    Holders Name	 	 
	 
	 	 	 	 
	 

	 	 

	 	 
	 
	 	 	 	 
	 

	 	 

	 	 
	 

	 	                    (Address)	 	 

     3. By its execution below and for the benefit of the Company, Holder hereby restates each of
the representations and warranties in Article 4 of the Warrant as the date hereof.

	 	 	 	 	 	 	 

	 	 	HOLDER:	 	 
	 
	 	 	 	 	 	 
	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 
	 	 

	 	 
	 

	 	Name:
	 	 

	 	 
	 

	 	 
	 	 

	 	 
	 

	 	Title:
	 	 

	 	 
	 

	 	 
	 	 

	 	 
	 

	 	(Date):
	 	 

	 	 
	 

	 	 	 	 

	 	 

 

 

APPENDIX 2

ASSIGNMENT

     For value received, Silicon Valley Bank hereby sells, assigns and transfers unto

	 	 	 

	Name:

	 	SVB Financial Group
	Address:

	 	3003 Tasman Drive (HA-200)
	 

	 	Santa Clara, CA 95054
	 
	 	 
	Tax ID:

	 	91-1962278

	 	 	that certain Warrant to Purchase Stock issued by KiOR, Inc., a Delaware corporation (the
“Company”), on March ___, 2009 (the “Warrant”) together with all rights, title and
interest, and obligations set forth therein.

	 	 	 	 	 	 	 

	 	 	SILICON VALLEY BANK	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:
	 	 

	 	 
	 

	 	 	 	 

	 	 

Date:                    

By its execution below, and for the benefit of the Company, SVB Financial Group makes each of
the representations and warranties set forth in Article 4 of the Warrant and agrees to all other
provisions of the Warrant as of the date hereof.

	 	 	 	 	 	 	 

	 	 	SVB FINANCIAL GROUP	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Name:
	 	 

	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:exv10w1

Exhibit 10.1

LOAN AGREEMENT

     THIS LOAN AGREEMENT, dated as of March 17, 2011, is between the Mississippi Development
Authority, acting for and on behalf of the State of Mississippi (the “Lender”) and KiOR Columbus,
LLC, a Delaware limited liability Company, (the “Borrower”).

W I T N E S S E T H:

     WHEREAS, the Lender agrees to make a loan to the Borrower under the Mississippi Industry
Incentive Financing Revolving Fund as authorized in House Bill 1701, 2010 Regular Session of the
Mississippi Legislature, in an amount not to exceed a total of Seventy Five Million Dollars
($75,000,000.00) for the purpose of reimbursement of costs incurred by the Borrower to purchase
land, to construct buildings and to purchase and install equipment for the manufacturing of
renewable crude oil from Mississippi-grown biomass (the “Loan”) as further set out in the
Memorandum of Understanding between Lender, KiOR, Inc., a Delaware corporation, and certain local
entities dated November 10, 2010 (the “MOU”); and

     WHEREAS, the Lender has determined that the Borrower and the Project as defined in the MOU do
qualify under the Mississippi Industry Incentive Financing Revolving Fund, as authorized in House
Bill 1701, 2010 Regular Session of the Mississippi Legislature (the “Laws”) and are eligible for
reimbursement of costs incurred by the Borrower to purchase equipment for use in the manufacture of
insulated glass units employing electrochromic technology; and

     WHEREAS, the Borrower has requested the Lender to finance a portion of the cost of such
acquisition of equipment; and

     WHEREAS, the Lender, by resolution, authorized the Loan pursuant to the Laws and the terms of
the MOU in the amount of Seventy Five Million Dollars ($75,000,000); and

     WHEREAS, the Borrower will execute a Note and a Security Agreement (both as hereinafter
defined) to evidence and secure its obligations to repay said Loan.

     NOW, THEREFORE, the parties hereto, intending to be legally bound hereby and in consideration
of the covenants hereinafter contained, do hereby agree as follows:

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ARTICLE I

DEFINITIONS

     Section 1.1. Definitions. The terms set forth below shall have the following meanings in
this Loan Agreement, unless the context clearly otherwise requires. Except where the context
otherwise requires, words importing the singular number shall include the plural number and vice
versa.

Agreement:

     “Agreement” shall mean this Loan Agreement as amended or supplemented from time to time in
accordance with the terms hereof.

Authorized Representative:

     “Authorized Representative” shall mean any person or persons from time to time designated to
act on behalf of the Borrower.

Business Day:

     “Business Day” shall mean any day, other than a Saturday or Sunday or official holiday of the
State of Mississippi, on which the Lender is not required or authorized by law to remain closed.

Borrower:

     “Borrower” shall mean KiOR Columbus, LLC , a Delaware limited liability company.

Cost or Cost of the Project:

     “Cost” or “Cost of the Project” in relation to this Loan shall mean and be deemed to include
reimbursable costs incurred by the Borrower to purchase land, to construct buildings and to
purchase and install equipment for use in the manufacturing of renewable crude oil from
Mississippi-grown biomass.

Deed of Trust

     “Deed of Trust” shall mean the deed of trust executed by the Borrower in favor of the Lender
and substantially in the form attached hereto as Exhibit “A” pledging the Project Site to secure
the Borrower’s obligation to repay the Loan pursuant to the terms hereof as amended from time to
time.

Event(s) of Default:

     “Event(s) of Default” shall mean any Event(s) of Default specified in Section 7.1 of this
Agreement.

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Facility:

     ‘Facility” shall mean the property, plant and equipment, including without limitation, the
Project, to be constructed in Columbus, Lowndes County, Mississippi, for the manufacturing of
renewable crude oil from Mississippi-grown biomass.

Loan:

     “Loan” shall have the meaning given such term in the first recitals paragraph of this
Agreement, or if the context requires, shall mean one or more advances made or to be made by the
Lender to the Borrower pursuant to the terms of this Agreement.

Loan Payments:

     “Loan Payments” shall mean the payments required to be made by the Borrower pursuant to
Section 4.2 hereof.

Note:

     “Note” shall mean the promissory note of the Borrower substantially in the form attached
hereto as Exhibit “B.”

Payment Date or Payment Dates:

     “Payment Date” or “Payment Dates” shall mean semi-annual payments due on the thirtieth day of
June and the thirty-first day of December of each year, provided, however, that if any such Payment
Date shall fall on a day other than a Business Day, the payment due on such Payment Date shall be
due on the next succeeding Business Day.

Person or person:

     “Person” or “person” shall mean, as the case may be, any individual, sole proprietorship,
corporation, partnership (including without limitation, general and limited partnerships), limited
liability company, joint venture, association, joint stock company, trust, unincorporated
organization or any government or any agency or political subdivision thereof, or public
corporation.

Project:

     “Project” shall mean costs associated with the acquisition of land described in Exhibit “C”,
together with the buildings and equipment to be situated thereon, for the manufacturing of
renewable crude oil from Mississippi-grown biomass and located at the Project Site.

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Project Site:

     “Project Site” shall mean the real property where the Project is situated, the street address
for which is 600 Industrial Park Access Road in Columbus, Lowndes County, Mississippi.

Security Agreement:

     “Security Agreement” shall mean the security agreement executed by the Borrower in favor of
Lender and substantially in the form attached hereto as Exhibit “D” to secure Borrower’s
obligation to repay the Loan pursuant to the terms hereof, as amended from time to time.

Transaction Documents:

     “Transaction Documents” shall mean this Agreement, the Note, the Security Agreement and all
other instruments and documents executed in connection herewith, each as amended from time to time.

State:

     “State” shall mean the State of Mississippi.

ARTICLE II

REPRESENTATIONS

     Section 2.1. Representations of Borrower. As of the date hereof, the Borrower makes the
following representations as the basis for the Loan by the Lender and the undertakings on the part
of the Borrower herein contained:

     (a) The Borrower is in good standing and is duly qualified to transact business in the State
of Mississippi, has the corporate power to enter into this Agreement and the Note and has duly
authorized the execution and delivery of this Agreement and the Note and as to the Borrower, this
Agreement and the Note are valid and legally binding and enforceable in accordance with their
respective terms, except to the extent the enforceability thereof may be limited (i) by bankruptcy,
reorganization, or similar laws limiting the enforceability of creditors’ rights generally or (ii)
by the availability of any discretionary equitable remedies.

     (b) The execution and delivery of this Agreement and the Note and the performance by Borrower
of its obligations under this Agreement or the Note do not violate any laws applicable to Borrower
in any material respect.

     (c) The estimated Cost of the Project is not less than the principal amount of the Loan.

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     (d) The Borrower will accept disbursements of Loan proceeds from Lender in accordance with the
provisions of this Agreement and will use or cause to be used, each such disbursement solely for
the Project.

     (e) All information furnished by the Borrower to the Lender for the purpose of approving the
Project and the financing of the Loan is true, accurate and complete in all material respects as of
the date provided, except with respect to projections and estimates as to future events, such
information is not to be viewed as facts and the actual results during the period or periods
covered by such projections and estimates may materially differ from the projected or estimated
results.

     (f) The Loan is not being made to finance any existing debt.

     (g) There are no undisclosed suits or proceedings pending or to the knowledge of the Borrower
threatened in writing against the Borrower which would reasonably be expected to have a material
adverse effect on the financial condition or business of the Borrower, and there are no undisclosed
proceedings by or before any governmental commission, board, bureau or other administrative agency
pending or to the knowledge of the Borrower, threatened in writing against the Borrower which
would reasonably be expected to have a material adverse effect on the financial condition or
business of the Borrower.

ARTICLE III

COMPLETION OF PROJECT

     Section 3.1. Completion of Project. The Borrower will complete the Project in accordance
with the purposes and as herein provided, will use commercially reasonable efforts to cause the
acquisition of land, buildings and equipment to be completed with all reasonable dispatch, but if
for any reason such acquisition shall not be completed there shall be no resulting diminution in or
postponement of the payments required in Section 4.2 hereof to be paid by the Borrower under this
Agreement and the Note.

     Anything in this Agreement notwithstanding, the Lender shall not be obligated to complete the
acquisition and installation of Project, other than to make the Loan.

     In order to effectuate the purposes of this Agreement, the Borrower will make, execute,
acknowledge and deliver, or cause to be made, executed, acknowledged and delivered, all contracts,
orders, receipts, writings and instructions, in the name of the Borrower or otherwise, with or to
other persons, firms or corporations, and in general do or cause to be done all such other things
as may be reasonably necessary, for completion of acquisition and installation of the Project and
fulfillment of the obligations of the Borrower under this Agreement.

     The Borrower will maintain such records in connection with the Project as to permit ready
identification thereof which records the Lender shall have the right to inspect upon reasonable
notice during regular business hours.

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     The Borrower will permit the Lender or any person designated by Lender upon reasonable notice
during regular business hours to inspect the land, buildings and equipment acquired pursuant to
this Loan.

     Section 3.2. Requisition for Project Funds. The Lender shall make disbursements to pay the
Cost of the Project, upon receipt by the Lender of (a) original executed requisitions (upon which
the Lender may rely conclusively and shall be protected in relying) signed by an Authorized
Representative, stating with respect to each payment to be made: (1) the requisition number, (2)
the name and address of the Person to whom payment is due or, in the event such payment is to
reimburse the Borrower, the name and address of the Person to whom payment previously has been
made, and proof thereof, (3) the amount that has been paid or is to be paid, (4) that there has
been no “Event of Default” under Section 7.1 of this Agreement by the Borrower under this
Agreement, and (5) that each obligation, item of cost or expense mentioned therein has been
properly incurred, and has not been the basis of any previous withdrawal; (b) copies of all
invoices or statements from a payee supporting each requisition for payment and clearly identifying
the equipment to be paid for or reimbursed. Documentation substantially in the form of the
attached Sample Requisition for Project Funds, together with the sample Purchase Requisition,
Invoices and Accounts Payable Inquiry Invoice Detail attached to the Sample Requisition for Project
Funds, all as set forth in the attached Exhibit “E”, shall be deemed to be in a form sufficient to
fully satisfy the requirements of this Section 3.2. Disbursements by the Lender may only be made
pursuant to the procedures outlined in this Section 3.2 to (1) Borrower to reimburse Borrower for
Costs paid by Borrower, or (2) directly to a vendor to pay for equipment being purchased by
Borrower in connection therewith.

     Requisition requests shall be made by the Borrower to the Lender between the first (1st) and
tenth (10th) day of a month and only during this time period, provided, however, that this
requirement will be deemed waived by the acceptance of the requisition request by the Lender.
Lender shall use its reasonable best efforts to fund all properly submitted requisition requests
within fifteen (15) days after submission.

ARTICLE IV

SECURITY; LOAN PAYMENTS; OTHER OBLIGATIONS

     Section 4.1. Transaction Documents. Concurrently with the signing of this Agreement, in
order to secure the obligations of the Borrower hereunder, the Borrower will execute and deliver
the Note, which shall be substantially in the form attached hereto as Exhibit “B,” the Deed of
Trust, which shall be dated the same date as this Agreement and substantially in the form attached
hereto as Exhibit “A” and which shall describe the Project Site and the Security Agreement, which
shall be dated the same date as this Agreement and substantially in the form attached hereto as
Exhibit “D,” and which shall include an item-by-item listing of all assets financed by Lender
pursuant to this
Agreement which are being pledged to secure the obligations of Borrower to Lender under this
Agreement, as well as a provision excluding all other assets of Borrower from any claims or liens
of Lender.

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     Section 4.2. Loan Payments. The principal payments on the Loan shall be due semi-annually
on the 30th day of June and the 31st day of December of each year in
installments sufficient to repay the total loan within a period of time determined by the weighted
average life of the equipment being purchased or twenty (20) years, whichever is less, commencing
on the earlier of December 31, 2012, or the next scheduled payment date that is at least six months
after the Start of Commercial Production (as defined in the MOU) (“weighted averaged life” shall
mean the result of finding the sum of the products produced by multiplying the cost of each piece
of Loan-financed equipment by its useful life and then dividing such sum by the total cost of all
Loan-financed equipment) . The entire amount of the outstanding principal balance and all other
applicable costs, charges or expenses is due and payable no later than the date which is twenty
(20) years from the date of the initial repayment of the loan proceeds hereunder by the Borrower.
Provided the first payment is prior to completion of Borrower’s annual financial statement audit,
Borrower will estimate the first payment and will perform a final payment calculation after
completion of the audit. Borrower will adjust the second payment to reflect any adjustment
resulting from the post-audit payment calculation. Equipment lives will be determined by applying
the capitalization and depreciation policy it uses for preparation of its audited financial
statements. Prior to the June payment each year, the payment amount will be recalculated based on
the principal amount due and owing at that time. All payments shall be payable in coin or currency
of the United States of America which, at the time of payment is legal tender for the payment of
the Loan and shall be made by the Borrower to the Lender by check delivered and received on payment
date or by bank wire or bank transfer as Lender may specify or approve.

     Section 4.3. Obligation to Make Payments Absolute. It is understood and agreed that all
payments by the Borrower under this Agreement and the Note shall be absolute and unconditional and
shall not be subject to any defense (other than payment) or any right of set-off, counterclaim or
recoupment.

     Section 4.4. Maintenance of Project. The Borrower will use commercially reasonable efforts
to maintain, preserve and keep the Project or cause the Project to be maintained, preserved and
kept, in good repair, working order and condition (subject to ordinary wear and tear) and will
from time to time make or cause to be made all necessary and proper repairs, replacements and
renewals.

     Section 4.5. Payment of Taxes and Assessments; Compliance with Law; No Further Liens. The
Borrower will: (a) pay, or make provision for payment of, all material lawful taxes and
assessments, including income, profits, property or excise taxes, if any, or other municipal or
governmental charges, levied or assessed by the Federal, state or any municipal government with
respect to or upon the Project or any part thereof or upon any payments hereunder when the same
shall become due, other than taxes and assessments that are being contested in good faith; and (b)
duly observe and comply with all valid requirements of any governmental authority necessary for the
operation of the Facility.

     Section 4.6. Operation of Project. The Borrower agrees that so long as the Loan is
outstanding, except (a) during periods (consisting of no more than thirty (30) consecutive calendar
days nor occurring no more often than once in any thirty-six (36) month period) during which
Borrower’s normal manufacturing operations at the Facility are halted because of reasons beyond

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Borrower’s reasonable control, or (b) during periods after the occurrence of damage or loss to the
Facility in excess of $250,000 during which Borrower has initiated and is diligently pursuing
efforts to rebuild and restore the Facility, Borrower will maintain or cause to be maintained the
operations of the Project, unless the Project is disposed of pursuant to Section 6.1 hereof.

     Section 4.7. Payment of Expenses. The Borrower will pay, or cause to be paid, in addition to
the payments provided for in Sections 4.2 and 4.3 hereof, all of the expenses of operation of the
Project, including, without limitation, the cost of all necessary and proper repairs, replacements
and renewals and any and all taxes and assessments payable pursuant to Section 4.5 hereof. The
Borrower further agrees to pay reasonable fees, expenses and charges incurred by Lender in making
the Loan, including but not limited to, the reasonable fees and out-of-pocket expenses of counsel
employed by the Mississippi Development Authority, but in all events, such payments by Borrower
shall be limited to Twenty-Five Thousand Dollars ($25,000.00).

     Section 4.8. Payments Continue Upon Destruction of Project. It is understood and agreed that
the payments under Section 4.2 hereof and on the Note and other charges payable hereunder shall
continue to be payable at the time and in the amounts herein specified (except in connection with a
prepayment permitted to be made under Section 8.1 hereof), whether or not the Project, or any
portion thereof, shall have been destroyed, wholly or partially, by fire or other casualty, and
that there shall be no abatement or diminution of any such payments and other charges by reason
thereof.

     Section 4.9. Release and Indemnification of the Lender. The Borrower hereby releases the
Lender from, and agrees that the Lender and its respective officers, directors, members, employees,
attorneys, and agents shall not be liable for, and agrees to defend, indemnify and hold the Lender
and its respective officers, directors, members, employees, attorneys, and agents harmless against:

     (a) any or all liability or loss, cost or expense, including reasonable attorneys’ fees,
resulting from or arising out of any loss or damage to property or any injury to or death of any
person occurring on or about the Project Site or resulting from any defect in the fixtures,
machinery, equipment or other property located on the Project Site or arising out of, pertaining
to, or having any connection with the Project or the financing thereof (whether or not arising out
of acts, omissions or negligence of the Borrower);

     (b) any and all claims, damages, judgments, penalties, costs, and expenses (including
reasonable attorneys’ fees and court costs now or hereafter arising from the aforesaid enforcement
of this paragraph) arising directly or indirectly from (i) the activities of the Borrower or any
third parties with whom Borrower has a contractual relationship, or (ii) the violation by the
Borrower of any environmental protection, health, or safety law in a material respect, whether any
such claims are
asserted by any governmental authority or any other Person which indemnity shall survive the
termination of this Agreement.

     Notwithstanding the foregoing, the release and indemnity provided for in this Section 4.9
shall not be effective to relieve the Lender or its respective officers, directors, members,
employees, attorneys and agents from damages that result from negligence or intentional misconduct
on the part

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of the Lender or from Lender’s failure to perform any obligation under (including
Lender’s obligation to fund Loans under this Agreement) or Lender’s breach of this Agreement. This
release and indemnification covenant shall survive the termination of this Agreement with respect
to liability arising out of any event or act occurring prior to such termination.

     Section 4.10. Insurance. Throughout the term of this Agreement, the Borrower shall keep, or
cause to be so kept, any buildings and contents of those buildings at the Project Site continuously
insured against such risks as are customarily insured against by businesses of like size and type
(other than business interruption insurance), paying or cause to be paid as the same become due all
premiums in respect thereto, including but not necessarily limited to:

     (a) Casualty insurance against loss and/or damage to any and all buildings and their contents,
including the equipment that is the subject of the Loan, at the Project Site under a policy or
policies covering such risks as are ordinarily insured against by similar businesses, including
without limiting the generality of the foregoing, fire, lightning, windstorm, hail, explosion, and
uniform standard extended coverage. Such insurance shall be for not less than the full insurable
value of the buildings and their contents, including the equipment that is the subject of the Loan.

     (b) Comprehensive general public liability insurance protecting the Borrower as a named
insured and the Lender as additional insured against liability for death and injuries to persons
and damage to property, occurring on, in or about the Project Site.

     (c) Workers’ compensation insurance respecting all employees employed at the Project Site in
such amount as is customarily carried by like organizations engaged in like activities of
comparable size and liability exposure.

     All insurance required hereby shall be taken out and maintained by Borrower in generally
recognized responsible insurance companies approved by the Borrower, which approval shall not be
unreasonably withheld. The insurance required may be contained in blanket policies now or
hereafter maintained or caused to be maintained or approved by the Borrower.

     Certificate or certificates of insurance showing that such insurance is in force and effect
shall be deposited with the Lender no later than the date on which Borrower shall take possession
of any property acquired with proceeds of the Loan. Prior to expiration of any such policy, the
Borrower shall furnish the Lender with evidence satisfactory to the Lender that the policy has been
renewed or replaced or is no longer required by this Agreement.

     Section 4.11. Application of Insurance Proceeds.

     (a) Immediately after the occurrence of any damage or loss to the Project Site in excess of
Two Hundred Fifty Thousand Dollars ($250,000.00) the Borrower shall notify the Lender as to the
nature and extent of such damage or loss. If the Borrower determines that rebuilding, repairing or
restoring the Project Site is practicable and desirable, the Borrower shall forthwith proceed with
such rebuilding, repairing or restoring the Project Site to its former condition or to a condition
that Borrower deems useful for the Project, and shall notify the Lender, upon the completion
thereof. In

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the event the Borrower elects to rebuild, repair or restore the Project Site, and the
net proceeds of insurance, if any, will be insufficient to pay in full the costs of rebuilding,
repairing or restoring the Project Site under this Section, the Borrower will nonetheless perform
such rebuilding, repairing or restoration.

     (b) If the Borrower chooses not to rebuild, repair or restore the Project Site, the Borrower
shall pay or cause to be paid to the Lender the proceeds of such insurance relating to the Project,
if any, to be applied to the repayment of the Loan.

     (c) Any provisions of this Agreement to the contrary notwithstanding, the Borrower shall be
entitled to receive, keep and retain that portion of insurance proceeds received for damages to its
own property other than, if an Event of Default has occurred and is continuing, the land, buildings
and equipment that is financed by the Loan. The Lender shall cooperate fully with the Borrower in
the handling and the conduct of any prospective or pending insurance claims.

ARTICLE V

SPECIAL COVENANTS

     Section 5.1. Agreement to Cooperate. In the event it may be necessary for the proper
performance of this Agreement, or for the exercise of any rights hereunder, on the part of the
Lender or the Borrower that any application or applications for any permit or license or
authorization to do or to perform certain things be made to any governmental or other agency by the
Borrower or the Lender, or both, the Borrower and the Lender each agree to execute and prosecute
upon the request of the other such application or applications except where the failure to obtain
any such permit or license or authorization would not have a material adverse effect on the Project
or such party’s ability to perform its obligations under this Agreement.

     Section 5.2. Covenant Against Waste. The Borrower shall use commercially reasonable efforts
to keep the Project Site clean and the buildings and the equipment therein in good repair (subject
to ordinary wear and tear), and to promptly comply with all laws, ordinances, regulations and
requirements of any governmental body affecting the Project Site, except where the failure to
comply would not reasonably be expected to have a material adverse effect on the Project Site.

     Section 5.3. Financial Statement Covenants. So long as the Borrower shall owe any amount
under this Agreement or the Note, the Borrower agrees that it shall furnish the Lender with
financial statements which may be consolidated statements of KiOR, Inc., prepared by a certified
public accountant in accordance with generally accepted accounting principles as of the close
of each fiscal year within one hundred and eighty (180) days after the close of such fiscal year.

     Section 5.4. Accounting Covenants. The Borrower covenants that it will maintain proper books
of record and account, in which full and correct entries regarding its business and affairs will be
made in accordance, to the extent applicable, with generally accepted accounting principles.

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     Section 5.5. Compliance with Environmental Laws. The Borrower shall use commercially
reasonable efforts to conduct all business, operations, and activities at or upon the Project Site
at all times during the term of this Agreement in material compliance with all applicable federal,
state, or local laws, ordinances, rules or regulations concerning public health, safety, or the
environment.

ARTICLE VI

ASSIGNMENT, LEASE AND SALE OF PROJECT

     Section 6.1. Disposal of Project and Assets by Borrower.

     This Agreement may be assigned in whole or in part, and the interest of the Borrower in the
Project, the Project Site and/or the Facility may be sold or leased as a whole or in part by the
Borrower, provided that any such assignee, vendee or lessee shall, in writing, specifically assume
the obligations and affirm in its own capacity and become liable for the representations,
warranties and covenants made by the Borrower in this Agreement or any Transaction Document, in
which case the Borrower shall no longer be liable for the performance and observance of the
obligations, agreements, representations, warranties and covenants made by the Borrower in this
Agreement or any Transaction Document, and Lender shall execute and deliver to Borrower
documentation sufficient to effectuate such release, subject, however, to the following conditions:

     (a) No sale, assignment or leasing of the Project shall relieve the Borrower from liability
for any of its obligations hereunder, and in the event of any such sale, assignment or leasing the
Borrower shall continue to remain primarily liable for the payments specified in Section 4.2 and
Section 4.3 hereof and for performance and observance of the other agreements on its part herein
provided, unless such sale, assignment or leasing of the Project is approved by the Lender, in
writing, which approval shall not be unreasonably withheld; and

     (b) In connection with such sale, assignment or leasing of the Project pursuant to this
Section 6.1, the Borrower shall, no later than ten (10) days prior to the effective date thereof,
furnish or cause to be furnished to the Lender a copy of each such proposed sale agreement,
assignment and lease, as the case may be, in substantially the form to be executed thereafter; and

     (c) In connection with such sale, assignment or leasing of the Project pursuant to this
Section 6.1, the Borrower shall, ten (10) days after the delivery thereof, furnish or cause to be
furnished to the Lender, a true and complete copy of each such executed sale agreement, assignment
and lease, as the case may be.

ARTICLE VII

EVENTS OF DEFAULT AND REMEDIES

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     Section 7.1. Events of Default. The following shall be “events of default” under this
Agreement, and the terms “event of default”, “Event of Default”, “default”, or “Default” shall
mean, whenever they are used in this Agreement, any one or more of the following events:

     (a) failure by the Borrower to pay or cause to be paid when due any Loan payment consisting of
principal required to be paid under Section 4.2 hereof and the Note, which failure shall have
continued for three (3) Business Days after written notice of such failure is delivered to
Borrower;

     (b) failure by the Borrower to pay when due any other payment required to be made under this
Agreement, which failure shall have continued for a period of ten (10) days after written notice
specifying such failure and requesting that it be remedied, is given to the Borrower by the Lender;

     (c) failure by the Borrower to observe and perform in any material way any covenant, condition
or agreement on its part to be observed or performed as set forth herein, other than as referred to
in subsections (a) and (b) of this Section 7.1, which failure shall have continued for a period of
forty-five (45) days after actual knowledge thereof by the Borrower or written notice, specifying
such failure and requesting that it be remedied, is given to the Borrower by the Lender; if by
reason of the nature of such failure the same can be remedied, but not within the said forty-five
(45) days, failure by the Borrower to proceed with reasonable diligence after receipt of said
notice or failure to continue with reasonable diligence its efforts to cure the same;

     (d) any material written representation or written warranty made by the Borrower in or with
respect to this Agreement or its application to the Lender for the Loan shall prove to have been
false in any material respect at the time of execution by the Borrower of this Agreement or said
application;

     (e) the Borrower shall commence a voluntary case or other proceeding in bankruptcy seeking
liquidation, reorganization, arrangement, readjustment of its debts or for any other relief under
the federal bankruptcy laws, as amended;

     (f) there shall be filed against the Borrower an involuntary petition in bankruptcy or seeking
liquidation, reorganization, arrangement, readjustment of its debts or any other relief under the
federal bankruptcy laws, as amended, and such involuntary petition remains undismissed for ninety
(90) consecutive days

     (g) failure by the Borrower to pay when due all amounts owed under Section 4.2(i) of the MOU
after KiOR, Inc. has defaulted on its investment commitment set out in Section 2.2(i) of the
MOU and after the Lender has given notice of its demand for the Borrower to make the payment
provided for in Section 4.2(i) of the MOU;

     (h) failure by the Borrower to pay when due all amounts owed under Section 4.2(ii) of the MOU
after KiOR, Inc. has defaulted on its expenditure commitment set out in Section 2.2(ii) of the MOU
and after the Lender has given notice of its demand for the Borrower to make the payment provided
for in Section 4.2(ii) of the MOU; or

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     (i) failure by the Borrower to pay when due all amounts owed under Section 4.3 of the MOU
after the Lender has given notice of its demand for the Borrower to make the payment provided for
in Section 4.3 of the MOU.

     Section 7.2. Remedies. Whenever any Event of Default referred to in Section 7.1 hereof shall
have occurred and be continuing, any one or more of the following remedial steps may be taken;
provided that written notice of the default has been given to the Borrower by the Lender, and the
default has not theretofore been cured.

     (a) The Lender may declare all unpaid loan payments and amounts due under the Note to be
immediately due and payable, whereupon the same shall become immediately due and payable.

     (b) The Lender may take any action at law or in equity, with respect to the equipment at the
Project Site which is financed by the Lender pursuant to this Agreement, including, without
limitation, to the extent applicable, to collect the payments then due and thereafter to become
due, or to enforce performance and observance of any obligation, agreement or covenant of the
Borrower under the Transaction Documents.

     Section 7.3. Power of Attorney. Borrower hereby constitutes and appoints Lender as its true
and lawful attorney-in-fact with full power of substitution until all obligations under this
Agreement (other than contingent indemnity obligations) to (i) perform Borrower’s obligations under
the Transaction Documents, (ii) to receive payment of and to endorse the name of Borrower to any
items of collateral subject to a lien in favor of Lender pursuant to the Security Agreement
(including checks, drafts and other orders for the payment of money) that come into Lender’s
possession or under Lender’s control, (iii) to file any claim or take any other action or institute
proceedings, either in its own name or in the name of Borrower or otherwise, which Lender may
reasonably deem necessary or appropriate to protect and preserve the right, title and interest of
Lender in and to such collateral, and (iv) to otherwise act with respect thereto as though Lender
were the outright owner of such collateral; provided, however, that the power of attorney granted
herein shall only be exercisable by Lender after the occurrence and during the continuation of an
Event of Default.

     Section 7.4. No Remedy Exclusive. No remedy conferred upon or reserved to the Lender by this
Agreement is intended to be exclusive of any other available remedy or remedies, but each and every
such remedy shall be cumulative and shall be in addition to every other remedy given under this
Agreement or now or hereafter existing at law or in equity or by statute. No delay or omission to
exercise any right or power accruing upon any default shall impair any such right or power or shall
be construed to be a waiver thereof, but any such right and power may be exercised
from time to time and as often as may be deemed expedient. In order to entitle the Lender to
exercise any remedy reserved to it in this Article VII, it shall not be necessary to give any
notice, other than such notice as may be herein expressly required.

     Section 7.5. Payment of Fees and Expenses. If the Borrower shall default under any of the
provisions of this Agreement and the Lender shall employ attorneys or incur other expenses for the
collection of the Loan payments or for the enforcement of performance or observance of any
obligation or agreement on the part of the Borrower contained in this Agreement, the Borrower will

13

 

on demand therefore pay the reasonable fees and expenses of the Lender, and their attorneys as they
are incurred including all reasonable fees of counsel including those incurred for negotiation,
trial, appeals of ruling of any lower tribunals, administrative hearings, bankruptcy and creditors’
reorganization proceedings.

     Section 7.6. Effect of Waiver. The Lender may waive any Event of Default under this
Agreement. In the event any agreement contained in this Agreement shall be breached and such
breach shall thereafter be waived, such waiver shall be limited to the particular breach so waived
and shall not be deemed to waive any other breach hereunder.

ARTICLE VIII

PREPAYMENT OF LOAN

     Section 8.1. Prepayment of Loan Payments. In the event the Borrower desires to prepay the
Loan, upon giving the Lender three (3) days written notice, the Borrower may pay all amounts
outstanding under this Agreement without penalty or premium and upon such payment, the Borrower
will have no further payment obligation hereunder and the Lender shall cancel and terminate the
Note. Upon Borrower’s payment of all outstanding obligations (other than contingent indemnity
obligations) under this Agreement pursuant to this Section 8.1 or otherwise, the security interest
granted to Lender on Borrower’s assets shall be terminated and released and Lender shall file any
UCC termination statements necessary to effect such termination and return any property held by
Lender in its possession as collateral and will execute and deliver to Borrower any additional
documents or instruments as Borrower shall reasonably request to evidence such termination.

ARTICLE IX

MISCELLANEOUS

     Section 9.1. Notices. All notices, certificates, requests or other communications hereunder
shall be sufficiently given and shall be deemed given when received by registered or certified
mail, return receipt requested (except as otherwise specified herein), postage prepaid; or when
received by overnight delivery; or when personally delivered; addressed as follows:

     If to the Lender:

Mississippi Development Authority

501 North West Street

Jackson, MS 39201

Post Office Box 849

Jackson, MS 39205

Attention: Kathy Gelston, CFO

Telephone Number: (601) 359-2902

14

 

Facsimile Number: (601) 359-1971

     If to the Borrower:

KiOR Columbus, LLC.

Attention: Fred Cannon

13001 Bay Park Road

Pasadena, TX 39205

Telephone Number: (281) 694-8700

Facsimile Number: (281) 694-8799

     Either Party may, by notice given under Section 9.1, designate any further or different
addresses to which subsequent notices, certificates, requests or other communications shall be
sent.

     Section 9.2. Parties Interested. This Agreement shall inure to the benefit of the Lender and
the Borrower and shall be binding upon the Lender and the Borrower and their respective successors
and assigns.

     No stipulation, obligation or agreement contained in this Agreement shall be deemed or
construed to be a stipulation, obligation or agreement of any present or future member, agent,
employee or official of the Lender in his individual capacity, and no present or future member,
agent, employee or official of the Lender shall be liable personally, for any breach or
non-observance or failure to comply with the above mentioned stipulations and obligations. No
present or future member, agent, employee or official of the Lender shall incur any personal
liability in acting or proceeding or in not acting or proceeding, in good faith, reasonably, under
the provisions of this Agreement.

     Section 9.3. Amendment to Agreement. Except as otherwise provided, this Agreement may not be
amended, changed, modified, altered or terminated without the prior approval of both parties. No
amendment, change, modification, or alteration of this Agreement shall be made other than pursuant
to a written instrument signed by the Lender and the Borrower.

     Section 9.4. Counterparts. This Agreement may be executed in any number of counterparts,
each of which, when so executed and delivered, shall be an original; but such counterparts shall
together constitute but one and the same Agreement.

     Section 9.5. Severability of Invalid Provisions. If any clause, provision or section of this
Agreement be held illegal or invalid by any court, the invalidity of such clause, provision or
section shall not affect any of the remaining clauses, provisions or sections hereof, and this
Agreement shall be construed and enforced as if such illegal or invalid clause, provision or
section had not been contained herein.

     Section 9.6. Governing Law. This Agreement shall be governed as to validity, construction
and performance by the laws of the State of Mississippi.

15

 

     IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be duly executed as of
the day and year first above written on the cover page hereof.

	 	 	 	 	 	 	 

	 	 	MISSISSIPPI DEVELOPMENT AUTHORITY	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Gary Swoope	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:
	 	Executive Director	 	 
	 
	 	 	 	 	 	 
	 	 	KiOR COLUMBUS, LLC.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:
	 	/s/ Fred Cannon	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:
	 	Chief Executive Officer	 	 

Attested:

	 	 	 

	/s/ G.E. Staggs
	 	 
	 

	 	 
	 
	 	 
	/s/ Connie Burke
	 	 
	 

	 	 

16

 

EXHIBIT A

 

 

 

Space Above Line for Official Use Only

Prepared by and Return to:

Waverly Harkins

Special Assistant Attorney General

Mississippi Development Authority

Post Office Box 849

Jackson, Mississippi 39205

601.359.2850

MS Bar No. 102380

Indexing Instructions: Fractional Section 32, Township 19 North, Range 18 East, Choctaw Meridian,
Lowndes County, Mississippi

DEED OF TRUST, FIXTURE FILING

AND ASSIGNMENT OF LEASES AND RENTS

FROM

KiOR Columbus, LLC, GRANTOR

13001 Bay Park Road

Pasadena, TX 77507

Attention: Fred Cannon, Chief Executive Officer

Telephone Number: (281) 694-8700

TO

Mississippi Development Authority, BENEFICIARY

501 North West Street

Jackson, Mississippi 39201

Post Office Box 849

Jackson, Mississippi 39205

Attention: Gary Swoope, Executive Director

Telephone Number: (6()1) 359-3449

A-1

 

DEED OF TRUST, FIXTURE FILING

AND ASSIGNMENT OF LEASES AND RENTS

     THIS DEED OF TRUST, FIXTURE FILING AND ASSIGNMENT OF LEASES AND RENTS (“Deed of Trust”) is
made and entered into as of the day of         ,
2011, by and among KiOR Columbus, LLC, a Delaware limited
liability company, hereinafter “Grantor”; Waverly Harkins, Special Assistant Attorney General,
Mississippi Development Authority, Post Office Box 849, Jackson, Mississippi 39205, hereinafter
“Trustee”; and Mississippi Development Authority, whose address is 501 North West Street, Jackson,
Mississippi 39201, hereinafter “Beneficiary.”

     Grantor is indebted to Beneficiary in the original principal amount of Seventy-Five Million
Dollars ($75,000,000.00) and such additional fees, costs and expenses as are set forth herein (the
“Loan”), and has agreed to pay the same, without interest thereon, according to the terms of the
Note (as defined in that certain Loan Agreement entered into by and between Grantor and Beneficiary
of even date herewith (the “Loan Agreement”)) made by Grantor to the order of Beneficiary and the
Loan Agreement, with final payment being due on or before 2031; and

     Grantor is executing this Deed of Trust to secure the Loan and all indebtedness and
obligations now or hereafter owed to Beneficiary by the Grantor incurred pursuant to this Deed of
Trust, the Note, the Loan Agreement or the Security Agreement (as defined in the Loan Agreement)
and all other documents and instruments now or hereafter evidencing, describing, or securing the
Loan or obligations contemplated hereby or delivered in connection herewith, as they may be
modified, amended, extended, renewed or substituted from time to time, including the unpaid
principal amount of the Loan, and all other obligations and liabilities of the Grantor to
Beneficiary, whether direct or indirect, absolute or contingent, due or to become due, or now
existing or hereafter incurred, that may arise under, or out of or in connection with the Loan, the
Note, the Security Agreement, this Deed of Trust, or any other Transaction Document (as defined in
the Loan Agreement) (collectively, the “Secured Obligations”);

     NOW THEREFORE, in consideration of the existing and future Secured Obligations and other good
and valuable consideration, Grantor hereby conveys and warrants unto Trustee, the property
described in Exhibit “A” attached hereto and made a part hereof, subject and subordinate
only to those matters more particularly set forth in Exhibit “B” attached hereto and made a
part hereof; together with any and all specific improvements and goods acquired by Grantor in whole
or in part with proceeds from the Loan, that are or may become fixtures now or hereafter located
thereon, or on any part or parcel thereof, and all additions, substitutions and replacements
thereof; and together with all rights, privileges, easements, rights of way, appurtenances,
streets, and roadways now or hereafter pertaining to the hereinabove described property (all of
which shall be collectively referred to herein as the “Property”). Any and all improvements and
goods located thereon, or on any parcel thereof, which are not acquired in whole or in part with
proceeds from the Loan are specifically excluded from the definition of “Property.”

A-2

 

     This conveyance is in trust to secure prompt payment and performance of the Secured
Obligations. If Grantor shall pay and perform the Secured Obligations, then this conveyance shall
be void and of no effect.

     Grantor and Beneficiary hereby agree as follows:

     Taxes; Insurance. Grantor shall cause to be paid when due any taxes and assessments,
general or special, and other obligations which may be levied or assessed upon the Property or
which, if not paid, may be asserted as a lien on the Property and all taxes on this Deed of Trust
or Beneficiary, hereinafter enacted arising out of this Deed of Trust or the indebtedness secured
hereby.

     Grantor shall cause to be maintained insurance at all times in accordance with the applicable
provisions of the Loan Agreement. All property damage and casualty insurance (or an endorsement
thereto) shall name the Beneficiary as an additional loss payee/mortgagee and all liability
insurance (or an endorsement thereto) shall name the Beneficiary as an additional insured. The
proceeds of any property or casualty insurance in respect of any casualty loss to any of the
Property shall be paid, held and applied in accordance with the applicable provisions of the Loan
Agreement. Grantor shall furnish the Beneficiary upon its request with certificates of insurance
and policies evidencing compliance with the foregoing insurance provision.

     In the event Grantor fails to cause said taxes and assessments to be paid or to cause the
Property to be insured, then Beneficiary may pay said taxes and assessments, redeem the Property
from any tax sale and insure the Property at the expense of Grantor but only after having given to
Grantor written notice of and a thirty (30) day period in which to cure such failure.

     In the event of loss or damage to the Property by fire or other hazard, Grantor will give
immediate notice to Beneficiary, who may make proof of loss if not made promptly by Grantor.

     Assignments of Leases and Rents. As additional security, Grantor hereby assigns to
Beneficiary all rents accruing on the Property. Grantor shall have the right to collect and retain
the rents until the occurrence of an Event of Default (as defined in the Loan Agreement). Upon the
occurrence of an Event of Default, Beneficiary in person, by an agent or by a judicially appointed
receiver shall be entitled to enter upon, take possession of and manage the Property and collect
the rents. All rents so collected shall be applied first to the costs of managing the Property and
collecting the rents, including fees for a receiver and an attorney, commissions to rental agents,
repairs and other necessary related expenses and then to payments on the amount of the Secured
Obligations then remaining unpaid.

     Maintenance of Property. Grantor agrees to cause the Property to be kept in the
condition required in the Loan Agreement and in compliance with all governmental laws, rules and
regulations and shall not permit or commit any removal, waste, impairment, deterioration,
demolition, alteration or abandonment thereof or permit any use of the Property in violation of any
law, in a manner which could invalidate any insurance on the Property, or which could result in an
uninsured loss.

A-3

 

     Advances. Beneficiary shall have the right, but not the obligation, to make any
payment or take any action for which Grantor is obligated hereunder, but only after having given to
Grantor written notice of and a thirty (30) day period in which to make such payment or take such
action. Any amount or expense, or other obligation paid or incurred by Beneficiary for or on behalf
of Grantor (including, but not limited to, taxes, assessments, and other obligations, insurance
premiums, expenses of managing the Property, costs of repairs or improvements, attorneys’ fees,
court costs and Trustee’s fees) shall be included within the definition of the term “Secured
Obligations,” shall be secured hereby and shall be due and payable by Grantor upon demand by
Beneficiary.

     Condemnation. Any and all judgments, awards of damages and settlements resulting from
any and all actual or threatened condemnation proceedings with respect to or for any damage
(whether caused by such condemnation or otherwise) to the Property or any part thereof shall be
disbursed and used in accordance with the terms of the Loan Agreement. Grantor shall promptly give
Beneficiary notice of any actual or threatened condemnation proceeding which may affect the
Property.

     Power of Sale. This conveyance, however, is in trust to secure the payment and
performance of the Secured Obligations. If an Event of Default has occurred then all of the Secured
Obligations shall, at the option of Beneficiary, be and become at once due and payable with notice
to Grantor, and Trustee shall, at the request and at the option of Beneficiary, sell the Property
or a sufficiency thereof, to satisfy the Secured Obligations at public outcry to the highest bidder
for Cash or on such other terms as Trustee may elect. “Cash” can include wire transfers, bank
checks and other forms of present payment acceptable to Trustee and Beneficiary. Sale of the
Property shall be advertised for three consecutive weeks preceding the sale in a newspaper
published in the county where the Property is situated, or if none is so published, then in some
newspaper having a general circulation therein, and by posting notice of sale for the same time at
the courthouse of the same county. The notice and advertisement shall disclose the names of the
original Grantor in this Deed of Trust. Grantor waives the provisions of Section 89-l-55 of the
Mississippi Code of 1972, and Section 111 of the Constitution of the State of Mississippi, as far
as such provisions restricts the right of Trustee to offer at sale more than 160 acres at a time,
and Trustee may offer the Property herein conveyed as a whole, regardless of how it is described.
If the Property is situated in two or more counties, or in two judicial districts of the same
county, Trustee shall have full power to select in which county, or judicial district, the sale of
the Property is to be made, newspaper advertisement published and notice of sale posted, and
Trustee’s selection shall be binding upon Grantor and Beneficiary. The Chief Financial Officer of
the Beneficiary may declare Grantor to be in default and request Trustee to sell the Property.
Beneficiary shall have the same right to purchase the Property at the foreclosure sale as would a
purchaser who is not a party to this Deed of Trust. At Beneficiary’s direction, Trustee can offer
and sell all or any part of the Property subject to any leases, easements or other encumbrances,
whether or not listed on Exhibit “B”. At any sale hereunder, Trustee may, from time to
time, adjourn said sale to a later time or date and from time to time and date to date without
readvertising the sale by giving notice of the time and place of such continued sale at the time
Trustee shall make said adjournment. Trustee shall have full power to conduct any sale hereunder
through an agent duly appointed by him for that purpose and said appointment need not be in writing
or recorded. Trustee may determine any details of sale not specified herein. Out of the proceeds
arising from said sale, the costs and expenses of preparing

A-4

 

the Property for and conducting the sale and enforcing this Deed of Trust, including a
reasonable Trustee’s fee, the attorneys’ fee prescribed in the Transaction Documents and this Deed
of Trust, and all reasonable costs and expenses of any person engaged to inspect the Property or to
examine or insure title thereto, shall first be paid, next, the amount of the Secured Obligations
then remaining unpaid shall be paid, and, lastly, any balance remaining shall be paid to Grantor or
to any other person lawfully entitled thereto. The power of sale granted hereunder may be
exercised, at Beneficiary’s discretion, as to all or any part of the Property. Neither institution
of suit on the Secured Obligations or any part thereof nor exercise of the power of sale granted
hereunder as to less than all of the Property shall affect this Deed of Trust as to the Property
not sold pursuant to the power of sale granted hereunder. Any facts stated in the notice of sale
and the trustee’s deed shall be deemed presumptively correct.

     Defeasance. If the Secured Obligations are paid and performed in full, Beneficiary
agrees to cancel this Deed of Trust upon the records. Grantor agrees to pay all usual and necessary
costs incident to such cancellation.

     Event of Default; Remedies. If an Event of Default shall have occurred and be
continuing or if at any time Beneficiary in good faith deems it necessary to protect its interest
under this. Deed of Trust, Beneficiary may, in addition to its ability to invoke the power of sale
provisions hereunder and to exercise the other remedies provided for in this Deed of Trust and
other Loan Documents, terminate Grantor’s license to collect and receive the rents, revenues and
profits, and, in addition, Beneficiary personally, by an agent or by judicially appointed receiver,
shall have the right to forthwith enter upon, take possession of and manage the Property or any
part thereof To the extent permitted by applicable law, Grantor waives notice of Beneficiary’s
application for a receiver and of the necessity of Beneficiary or the receiver posting bond. The
rents, revenues and profits shall be applied, first, to the costs incurred by Beneficiary and its
agents and contractors in managing the Property or any part thereof and collecting the rents,
revenues and profits, including fees and commissions to agents and attorneys, and the costs of any
repairs and expenses incurred by Beneficiary in leasing or preparing the Property or any part
thereof for lease and then to the Secured Obligations in such manner as Beneficiary may elect. All
remedies provided to Beneficiary under this Deed of Trust are cumulative and not exclusive and are
in addition to any other remedies available to Beneficiary by agreement or applicable law.

     Appointment of Successor Trustee. Beneficiary may without notice to any party to this
Deed of Trust or to their successors or assigns, and without regard to the willingness or inability
of Trustee to act, or to execute this trust, appoint another person or succession of persons to act
as trustee herein, and such appointee or substitute shall have all the title, authority and powers
in the execution and enforcement of this trust as are vested in Trustee. If Beneficiary be a
corporation or other entity, such appointment may be made by any one of its officers, agents or
other persons authorized to act on behalf of the entity. No one exercise of this power of
appointment, the power of sale, or any other power or right given in this Deed of Trust shall
exhaust the right to exercise such power, but all rights and powers herein given may be exercised
as often as may be necessary to achieve the collection of all amounts and the performance of all
Secured Obligations secured by this Deed of Trust until said amounts and Secured Obligations are
fully, finally and indefeasibly paid and discharged. Trustee shall not be liable for any error of
judgment or act done by Trustee in good faith. Trustee shall have the right to resign at any time.

A-5

 

     First Lien; Subordinate Indebtedness. Any Secured Obligation at any time secured
hereby may be extended, rearranged or renewed without in anywise altering, varying or diminishing
the force, effect or lien of this Deed of Trust. Grantor shall not create or suffer to exist any
lien of any nature on the Property other than a lien for ad valorem taxes not yet due and payable,
the lien of this Deed of Trust. If Grantor shall, with Beneficiary’s prior written consent, grant
or there shall otherwise be created any lien of any nature on the Property junior to this Deed of
Trust, Grantor shall perform its obligations under such junior lien. Further such junior lien shall
be subject to the condition that the time for the payment of the Secured Obligations hereby secured
and the manner and amount of payment thereof, the benefits of the security afforded hereby or any
obligation contained in an instrument substituted therefor, may, without the consent of such junior
lienholder, and without any obligation to give notice of any kind thereto, be changed, increased,
extended or suspended on any terms whatsoever.

     Successors and Assigns. The agreements herein contained shall be binding upon Grantor
and its heirs, executors, administrators, successors, and assigns and inure to the benefit of
Beneficiary and its successors and assigns.

     Further Assurances. Grantor, upon request of Beneficiary, will execute and file any
further documents as may be necessary, desirable or proper to correct any defect, error or omission
which may be discovered herein or in any other document executed in connection herewith, to carry
out more effectively the purposes of this Deed of Trust or to subject to the lien and security
interest hereof any property intended to be covered hereby.

     Pronouns. Whenever used herein, the singular number shall include the plural, the
plural the singular, the use of any gender shall be applicable to all genders, and the term
“Beneficiary” shall include any payee of the Note secured hereby or any legal holder or other
transferee thereof whether by operation of law or otherwise. Whenever used herein, the term
“Grantor” shall include all grantors collectively and any one of the grantors individually, and all
liability shall be joint and several.

     Governing Law. This Deed of Trust shall be governed by the laws of Mississippi and the
applicable laws of the United States of America.

     Severability. The unenforceability or invalidity of any provision(s) of this Deed of
Trust shall not render any other provision(s) hereof unenforceable or invalid.

     Notices. All notices and other communications required or permitted to be given
pursuant to this Deed of Trust (except for notices of a foreclosure sale which shall be given in
the manner set forth above) shall be given in the same manner, to the same addresses and shall be
deemed delivered, all as set forth in the Loan Agreement.

     Nonwaiver. A failure on the part of Beneficiary to exercise any remedy or option
contained in this Deed of Trust in the Event of Default shall not constitute a waiver of
Beneficiary’s right to exercise said remedy or option in the event of any subsequent default.

     Entire Agreement; Amendment. This Deed of Trust, the Loan Agreement and other
Transaction Documents contain the entire agreement between Grantor and Beneficiary relating to the
subject matter hereof and all prior agreements related thereto which are not

A-6

 

contained herein are terminated. This Deed of Trust may be amended, revised, waived,
discharged, released or terminated, in whole or in part, only by a written instrument executed by
the party against which enforcement of the amendment, revision, waiver, discharge, release or
termination is asserted.

     Counterparts. This Deed of Trust may be executed in any number of counterparts, each
of which shall be an original but all of which together shall constitute but one instrument.

     Definitions. All capitalized terms used herein without definition shall have the
respective meanings provided therefor in the Loan Agreement.

     Fixture Filing. This Deed of Trust is also a financing statement filed as a fixture
filing as to goods that are or may become fixtures related to the Property.

     Release of Collateral. Beneficiary can release all or part of the Property and the
Fixtures from the security interest created by this Deed of Trust without releasing Grantor or any
guarantor from any liability under any of the Secured Obligations or any guaranty of any of the
Secured Obligations.

     Waiver of Marshalling. Grantor disclaims and waives any obligation of Beneficiary to
marshal assets or sell in the inverse order of alienation in the course of Beneficiary exercising
its rights under the Loan Documents.

     IN WITNESS WHEREOF, Grantor has executed this instrument on the date beneath its signature and
effective as of the date first above written.

	 	           	 	 	 	 	 
	 	 	GRANTOR:
	 
	 	 	 	 	 	 
	 
	ATTEST:	 	KiOR COLUMBUS, LLC
	 

	 	By:	 	 	 	 
	 
	 	 	 	 

	 	 	Title.	 	 
	 

	 	 	 	 	 	 

	 

	 	Date:	 	 	 	 
	 

	 	 	 	 	 	 

A-7

 

STATE OF                     

COUNTY OF                     

     Personally appeared before me, the undersigned authority in and for the said county and state,
on this the _________ day of ______________, 2011, within my jurisdiction, the within named,
_________________________ who acknowledged that he/she is manager of KiOR COLUMBUS, LLC, a Delaware
limited liability company, and that for and on behalf of said limited liability company, and as its
act and deed, he/she executed the above and foregoing instrument, after first having been duly
authorized by said limited liability company so to do.

	 	 	 	 	 
	 
	 
	 	
 

NOTARY PUBLIC

 	 
	 	 	 
	 	 	 
	 	 	 
	 

My Commission Expires:

(SEAL)

A-8

 

EXHIBIT “A”

LEGAL DESCRIPTION

A-9

 

[ATTACH PERMITTED EXCEPTIONS]

EXHIBIT “B”

A-10

 

EXHIBIT B

PROMISSORY NOTE

			
	 	 	 
	Date: _______________, 2011
	 	$75,000,000.00

     FOR VALUE RECEIVED, Kior, Columbus, LLC., (the “Borrower”), hereby promises to pay to the
order of the Mississippi Development Authority (the “Lender”) or its assigns, the principal sum of
Seventy Five Million Dollars ($75,000,000.00) until fully and finally paid, and all other amounts
payable by the Borrower under the Loan Agreement (as hereinafter defined).

     This Note has been executed under and pursuant to a Loan Agreement dated as of this date
between the Lender and the Borrower (the “Agreement”), which Agreement is incorporated herein in
its entirety by reference. This Note is issued to evidence the obligation of the Borrower under
the Agreement to repay the loan made by the Lender and all other payments of any kind required to
be paid by the Borrower under the Agreement. The Agreement includes provisions for prepayment and
acceleration of this Note. In the event that the terms of this Note conflict with the terms of the
Agreement, the terms of the Agreement shall control.

     The principal payments on the Loan shall be due semi-annually on the 30th day of
June and the 31st day of December of each year in installments sufficient to repay the
total loan within a period of time determined by the weighted average life of the equipment being
purchased or twenty (20) years, whichever is less, commencing on the earlier of December 31, 2012
or the next scheduled payment date that is at least six months after the Start of Commercial
Production (as defined in the MOU) (“weighted averaged life” shall mean the result of finding the
sum of the products produced by multiplying the cost of each piece of Loan-financed equipment by
its useful life and then dividing such sum by the total cost of all Loan-financed equipment). The
entire amount of the outstanding principal balance and all other applicable costs, charges or
expenses is due and payable no later than the date which is twenty (20) years from the date of the
initial repayment of the loan proceeds hereunder by the Borrower. Provided the first payment is
prior to completion of Borrower’s annual financial statement audit, Borrower will estimate the
first payment and will perform a final payment calculation after completion of the audit. Borrower
will adjust the second payment to reflect any adjustment resulting from the post-audit payment
calculation. Equipment lives will be determined by applying the capitalization and depreciation
policy it uses for preparation of its audited financial statements. Prior to the June payment
each year, the payment amount will be recalculated based on the principal amount due and owing at
that time. All payments shall be payable in coin or currency of the United States of America
which, at the time of payment is legal tender for the payment of the Loan and shall be made by the
Borrower to the Lender by check delivered and received on payment date or by bank wire or bank
transfer as Lender may specify or approve.

     As provided in the Agreement and subject to the provisions thereof, payments hereon are to be
made at the principal office of the Lender as shown in the Agreement in an amount which

B-1

 

together with other monies available therefore pursuant to the Agreement, will equal the
amount payable as principal due on the Loan (as defined in the Agreement) on such due dates.

     The Borrower shall make payments on this Note on the dates and in the amounts as calculated
each year as provided herein and in the Agreement and in addition shall make such other payments as
are required pursuant to the Agreement. Upon the occurrence and during the continuance of an Event
of Default, as defined in the Agreement, the principal on this Note may be declared immediately due
and payable as provided in the Agreement. Upon any such declaration the Borrower shall pay all
costs, disbursements, expenses and reasonable counsel fees of the Lender in seeking to enforce
their rights under the Agreement and this Note.

     The Borrower (a) waives diligence, demand, presentment for payment, notice of nonpayment,
protest and notice of protest, notice of any renewals or extension of this Note, and (b) agrees
that the time for payment of this Note may be extended at the sole discretion of the Lender without
impairing the Borrower’s liability hereon. Any delay on the part of the Lender in exercising any
right hereunder shall not operate as a waiver of any such right, and any waiver granted with
respect to one default shall not operate as a waiver in the event of any subsequent or continuing
default.

     This Note shall be governed and construed in accordance with the laws of the State of
Mississippi.

     IN WITNESS WHEREOF, the undersigned has caused this Note to be executed in its name and, if
applicable, its corporate seal to be hereunto affixed and attested to by its duly authorized
officers all as of the day and year first above written.

	 	 	 	 	 	 	 

	 	 	KIOR COLUMBUS, LLC	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 

	 	 

Attested:

	 	 	 

	 

	 	 
	 
	 	 
	 

	 	 

B-2

 

GUARANTY

     For value consideration received and in consideration for and as an inducement to the Lender
to advance credit to the Borrower under the foregoing Note, the undersigned, KiOR, Inc., a Delaware
corporation (“Guarantor”) as the sole member of the Borrower, does hereby absolutely and
unconditionally guarantee to the Lender, its successors and assigns, the full performance and
observance of all of the obligations, covenants and agreements therein made by Borrower, without
requiring any notice of nonpayment, nonperformance, or nonobservance, or proof, or notice, or
demand, whereby to charge Guarantor therefore, all of which Guarantor hereby expressly waives.
Guarantor further covenants and agrees that this guaranty shall remain in force and effect as to
any renewal, modification, or extension of the foregoing Note. Guarantor subordinates any and all
claims which Guarantor has or may have against the Borrower by reason of subrogation for payments
or performance under this Guaranty or claims for any other reasons or cause. Guarantor agrees not
to assert any claim which it has or may have against the Borrower, including claims by reason of
subordination under this Guaranty, until such time as the obligations of the Borrower to the Lender
under the foregoing Note are fully satisfied and discharged. Guarantor waives trial by jury with
respect to any action, claim, suit or proceeding in respect of or arising out of this Guaranty.
This Guaranty is binding upon Guarantor, its successors, legal representatives and assigns, and is
binding upon and shall inure to the benefit of the Lender and its successors, legal representatives
and assigns.

     This Guaranty is a guaranty of payment, and not a guaranty of collection. Guarantor shall pay
any such obligations as an obligation for payment due and owing directly from Guarantor to the
Lender without any abatement, reduction, setoff, defense, counterclaim or recoupment.

     The obligations of Guarantor hereunder are absolute, unconditional and irrevocable, and may
not be cancelled, terminated, repudiated or rescinded for any reason. Guarantor shall not be
released from any obligations under or in respect of this Guaranty for any reason, nor shall such
obligations be reduced, diminished or discharged for any reason, including:

     (a) Modifications; Indulgences; Payment Applications. Any modifications, renewals, or
alterations of the Loan Agreement, Promissory Note or any other agreement, document or instrument
relating to any obligation; any indulgences, adjustments, preferences, extensions or compromises
made by Borrower in favor of Lender; or the application of any payments and receipts, by whomever
paid and/or however realized, to any amounts owing by the Borrower to Lender in such manner as
Lender shall determine in its sole discretion.

     (b) Condition of Borrower or Guarantor. Any insolvency, bankruptcy, arrangement,
adjustment, composition, liquidation, disability, dissolution, appointment of a receiver for, or
other similar proceeding affecting Borrower or Guarantor.

     (c) Invalidity of Obligations or Other Agreements. The invalidity, illegality or
unenforceability of any obligation for any reason whatsoever (excluding any invalidity, illegality
or unenforceability attributable to Lender), including, but not limited to: the existence of valid
defenses (other than the full and indefeasible payment or performance of such Obligation),
counterclaims or off-sets to any Obligation; the violation of applicable usury or other laws by any
Obligation; or the lack of authenticity or genuineness of any document or instrument relating

B-3

 

to the Obligations (excluding any lack of authenticity or genuineness attributable to Lender).
This Guaranty shall be in addition to any other guaranty or other security for the Obligations, and
it shall not be prejudiced or rendered unenforceable by the invalidity or unenforceability of any
such other guaranty or security.

     IN ALL RESPECTS, INCLUDING ALL MATTERS OF CONSTRUCTION, VALIDITY, AND PERFORMANCE, THIS
AGREEMENT SHALL BE GOVERNED BY, CONSTRUED, AND ENFORCED IN ACCORDANCE WITH THE LAWS OF THE STATE OF
MISSISSIPPI, WITHOUT REGARD TO CONFLICTS OF LAW PRINCIPLES, AND ANY APPLICABLE LAWS OF THE UNITED
STATES OF AMERICA. Time is of the essence in the payment and performance of all obligations and all
of the Guarantor’s obligations and liabilities owing to Lender hereunder.

March                     , 2011

	 	 	 	 	 	 	 

	 	 	KiOR, INC.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	 	 	 

	 	 
	 
	 	 	 	 	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 

	 	 

B-4

 

EXHIBIT C

Tract I

A TRACT OF LAND CONTAINING 22.35 ACRES, MORE OR LESS, BEING SITUATED IN FRACTIONAL SECTION 32,
TOWNSHIP 19 NORTH, RANGE 18 EAST, LOWNDES COUNTY, MISSISSIPPI, AND BEING MORE PARTICULARLY
DESCRIBED AS FOLLOWS:

Commencing at a found rebar at the Northwest corner of Section 32, Township 19 North, Range 18
East, thence run South for a distance of 2,652.19 feet to a point, thence run East for a distance
of 2,366.91 feet to a found U.S. Army Corps of Engineers (USACE) monument (unstamped), and being
the Point of Beginning; thence run S 03°18’48” W for a distance of 272.63 feet to a USACE monument
stamped “802-2”, thence run S 23°57’40” E for a distance of 492.42 feet to a USACE monument stamped
“802-3”, thence run S 37°51’17” W for a distance of 570.19 feet to a USACE monument stamped
“802-4”, thence run S 32°45’20” E for a distance of 281.80 feet to a USACE monument stamped
“802-5”, thence S 89°57’11” E for a distance of 475 feet more or less to point on the right bank of
the Tombigbee River, thence run Northeasterly along said right bank of the river for a distance of
1485 feet more or less to a set iron pin; thence leaving said right bank of the river, run S 8 line
of a paved county road known as Industrial Park Road; thence run along 9°24’15” W for a distance of
625.71 feet to a found iron pin on the East right-of-way said right-of-way line and being along a
curve to the left having a radius of 100.0 feet with a chord bearing and distance of N 36°42’22” W,
109.05 feet and a arc length of 115.28 feet to a concrete right-of -way marker; thence, leaving
said right-of-way line, run S 80°18’21” W for a distance of 100.0 feet to a set iron pin on the
West right-of-way line of said Industrial Park Road; thence along said right-of-way line, run N
09°41’39” W for a distance of 62.92 feet to a set iron pin; thence leaving said right-of-way line,
run along a curve to the right having a radius of 105.47 feet with a chord bearing and distance of
S 82°32’08” W, 85.15 feet and a arc length of 87.66 feet to a set iron pin; thence run S 74°40’19”
W for a distance of 203.18 feet to a set iron pin; thence run N 08°32’01” W for a distance of
118.16 feet to a set iron pin; thence run West for a distance of 53.17 feet to the Point of
Beginning.

C-1

 

Tract II

A TRACT OF LAND CONTAINING 7.43 ACRES, MORE OR LESS, BEING SITUATED IN FRACTIONAL SECTION 32,
TOWNSHIP 19 NORTH, RANGE 18 EAST, LOWNDES COUNTY, MISSISSIPPI, AND BEING MORE PARTICULARLY
DESCRIBED AS FOLLOWS:

Commencing at a found rebar at the Northwest corner of Section 32, Township 19 North, Range 18
East, thence South a distance of 2,652.19 feet to a point, thence East a distance of 2,236.58 feet
to a set iron pin and being the Point of Beginning; thence run S 00°13’12” E for a distance of
129.31 feet to a set iron pin; thence run S 21°21’06” W for a distance of 129.31 feet to a set iron
pin; thence run S 61°23’59” E for a distance of 103.72 feet to a set iron pin; thence run S
41°27’45” E for a distance of 147.15 feet to a set iron pin; thence run S 2419’13” E for a distance
of 172.50 feet to a set iron pin; thence run S 02°59’42” W for a distance of 65.26 feet to a set
iron pin; thence run S 29°12’30” W for a distance of 209.55 feet to a set iron pin; thence run S
47°14’21” W for a distance of 167.07 feet to a set iron pin; thence run S 65°05’45” W for a
distance of 132.71 feet to a set iron pin; thence run S 32°00’28” W for a distance of 72.44 feet to
a set iron pin; thence run S 01°16’22” E for a distance of 128.88 feet to a set iron pin; thence
run S 37°44’27” E for a distance of 616.88 feet to a set iron pin; thence run S 62°31’04” E for a
distance of 138.97 feet to a set iron pin; thence run S 89°57’11” E for a distance of 260.76 feet
to a set iron on the right bank of the Tombigbee River; thence run along said right bank for the
following calls and distances, N 10°20’03” E for a distance of 142.83, N 02°36’53” E for a distance
of 115.40 feet, N 07°58’05” E for a distance of 61.71 feet; thence leaving said right bank run N
89°57’11” W for a distance 512.68 feet to a U.S.
Army Corps of Engineers (USACE) monument stamped
“802-5”; thence run N 32°45’20” W for a distance of 281.80 feet to a USACE monument stamped
“802-4”; thence run N 37°51’17” E for a distance of 570.19 feet to a USACE monument stamped
“802-3”; thence run N 23°57’40” W for a distance of 492.42 feet to a USACE monument stamped
“802-2”; thence run N 03°18’48” E for a distance of 272.63 feet to a USACE monument (not stamped);
Thence run West for a distance of 130.33 feet to the Point of Beginning.

C-2

 

EXHIBIT D

PURCHASE MONEY SECURITY AGREEMENT

D-1

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