Document:

exv4w13

Exhibit 4.13

AMENDMENT NO. 2

Dated February 28, 2011

          THIS AMENDMENT NO. 2 (“Amendment 2”) to that certain Loan and Security Agreement No. 1452
dated as of January 27, 2010 (“Agreement”), by and between Lighthouse Capital Partners VI,
L.P., as “Agent” for the lenders identified on Schedule A to the Agreement (such lenders,
together with their respective successors and assigns are referred to herein each individually as a
“Lender” and collectively as “Lenders”), the Lenders and Kior, Inc. (“Borrower”).

RECITALS

          WHEREAS, Borrower and Lenders have previously entered into that certain Loan and Security
Agreement No. 1452 dated January 27, 2010, as amended, (the “Agreement”) (all capitalized terms not
otherwise defined herein are defined in the Agreement);

          WHEREAS, Borrower has requested that Lenders modify certain terms of its existing term loan
financing; and

          WHEREAS, Lenders have agreed to do so under the Agreement, subject to all of the terms and
conditions hereof and of the Agreement.

          NOW, THEREFORE, in consideration of the foregoing and the mutual covenants herein contained,
the parties
hereby agree to modify the Agreement and to perform such other covenants and conditions as follows:

     I. Section 1.1, the following definitions shall be added to the Agreement:

“Amendment 1” means that certain Amendment No. 1 to Loan and Security Agreement by and between
Agent, Lenders and Parent.

“Amendment 2” means this Amendment No. 2 to Loan and Security Agreement by and between Agent,
Lenders and Borrower.

“Columbus” means Kior Columbus LLC, a limited liability company organized under the laws of
Delaware and a wholly-owned subsidiary of Borrower.

“Exempt Subsidiary” means (i) Columbus and (ii) each Subsidiary formed after the date hereof that
is the primary obligor to the United States Department of Energy under one or more credit
arrangements for the development of alternative fuel projects.

“New Warrants” means the warrant agreements in the form attached to this Amendment 2 as Exhibit
C-2.

     II. Section 1.1, the following definitions of the Agreement shall be deleted in their entirety
and replaced with the following:

“Basic Rate” a per annum rate of interest equal to (i) 13% during the Interest Only Period and (ii)
12% on and after the Loan Commencement Date.

“Commitment Fee” means (i) $15,000 due in conjunction with the Agreement; and (ii) $15,000 due in
conjunction with this Amendment 2.

“Disclosure Schedule” means the updated schedule attached as Schedule 1-1 hereto.

 

 

“Loan Documents” means, collectively, the Agreement, Amendment 1, Amendment 2, the Warrant, the
Notes, and all other documents, instruments and agreements entered into between Borrower or any
Subsidiary or affiliate of Borrower and Lender in connection with the Loan, all as amended or
extended from time to time.

“Incumbency Certificate” means the document in the form of Exhibit E attached to the Agreement for
Parent and in the form of Exhibit E-1 attached to this Amendment 2.

“Interest Only Period” means the period commencing on February 1, 2011 and continuing through the
day immediately preceding the Loan Commencement Date.

“Loan Commencement Date” means , March 1, 2012.

“Note” means collectively (i) the Amended and Restated Secured Promissory Note (the “LCP Amended
Note”) in the form of Exhibit B-1 attached to Amendment 2, which shall amend and restate the Note
issued by Borrower to Lighthouse Capital Partners VI, L.P. on January 29, 2010 in the principal
amount of $4,900,000; and (ii) (A) the Amended and Restated Secured Promissory Note (the “Leader-A
Amended Note”) in the form of Exhibit B-2 attached to Amendment 2, which shall amend and restate
the Note issued by Borrower to Leader Lending, LLC — Series A on January 29, 2010 in the principal
amount of $1,050,000 and (B) the Amended and Restated Secured Promissory Note (the “Leader-B
Amended Note”) in the form of Exhibit B-3 attached to Amendment 2, which shall amend and restate
the Note issued by Borrower to Leader Lending, LLC — Series B on January 29, 2010 in the principal
amount of $1,050,000.

“Permitted Indebtedness” means: (i) the Loan; (ii) unsecured trade debt incurred in the ordinary
course of Borrower’s or any Subsidiary’s business; (iii) Indebtedness secured by clauses (ii), (v),
and (vi) of Permitted Liens; (iv) Indebtedness between the Borrower and any Exempt Subsidiary
created in the ordinary course of business (for clarity, for purposes of this section, the
“ordinary course of business” shall include such intercompany Indebtedness incurred for purposes of
funding the expenses related to the financing, buildout, development and operation of the business
of such Exempt Subsidiary); (v) Indebtedness between the Borrower and any Subsidiaries that are not
Exempt Subsidiaries created in the ordinary course of business, provided such Subsidiary is a
co-Borrower hereunder; (vi) Indebtedness set forth on the Disclosure Schedule as of the date of
this Agreement; (vii) Subordinated Indebtedness; (viii) unsecured guarantees of Borrower made with
respect to the primary obligations of its Exempt Subsidiaries including obligations of the Exempt
Subsidiaries in favor of the State of Mississippi and in the future the United States Department of
Energy, provided such primary obligations of the Exempt Subsidiary and the corresponding Borrower
guaranty agreements are all in form and substance reasonably satisfactory to Lender; and (ix)
extensions, refinancing, modifications, amendments and restatements of any items of Permitted
Indebtedness above, provided that the principal amount thereof is not increased or the terms
thereof are not modified to impose more burdensome terms upon Borrower or an Exempt Subsidiary, as
the case may be.

“Permitted Investments” means (i) Investments existing as of the date hereof and disclosed on the
Disclosure Schedule; (ii) (a) marketable direct obligations issued or unconditionally guaranteed by
the United States of America or any agency or any State thereof maturing within 1 year from the
date of acquisition thereof, (b) commercial paper maturing no more than one year from the date of
creation thereof and currently having a rating of at least A-2 or P-2 from either Standard & Poor’s
Corporation or Moody’s Investors Service, (c) certificates of deposit maturing no more than 1 year
from the date of investment therein, and (d) money market accounts; (iii) Investments made pursuant
to an investment policy approved by the Board of Directors that is designed to maintain liquidity
and preserve capital with respect to Borrower’s excess cash; (iv) Investments not to exceed
$100,000 in the aggregate in any fiscal year consisting of (a) travel advances and employee
relocation loans and other employee loans and advances in the ordinary course of business and (b)
loans to employees, officers and directors relating to the purchase of equity securities of
Borrower pursuant to employee stock purchase plan agreements approved by Borrower’s Board of
Directors; (v) Investments (including debt obligations) received in connection with the bankruptcy
or reorganization of customers or suppliers and in settlement of delinquent obligations of, and
other disputes with, customers or suppliers arising in the ordinary course of Borrower’s business;
(vi) Investments consisting of notes receivable of, or prepaid royalties and other credit
extensions, to customers and suppliers who are not affiliates, in the ordinary course of business;
and (vii) deposit accounts maintained by Borrower in the ordinary
course of business; (viii) Investments by Borrower into Subsidiary (including without limitation
the

 

 

Exempt Subsidiaries) or by a Subsidiary into another Subsidiary to fund such Subsidiary’s
ordinary course operations (for clarity, for purposes of this section, the “ordinary course
operations” shall include operations related to the financing, buildout, development and operation
of the business of such Exempt Subsidiary, including the Indebtedness of the Exempt Subsidiaries in
favor of the State of Mississippi and in the future the United States Department of Energy).

“Subsidiary” means any entity of which a majority of the outstanding capital interest entitled to
vote for the election of directors (otherwise than as the result of a default) is owned by Borrower
directly or indirectly through Subsidiaries, including any Exempt Subsidiary.

     “Warrant” or “Warrants” means the Warrant in favor of each of the Lenders and its affiliates
to purchase securities of Borrower substantially in the form of Exhibit C attached to the Agreement
and the New Warrants in the form of that of Exhibit C-2 attached to this Amendment 2.

     III. Section 5 of the Agreement. Section 5.3 of the Agreement shall be deleted and replaced
with the following:

5.3 Disclosure Schedule. All information on the Disclosure Schedule is true, correct and complete
as of the date of this Amendment 2.

     IV. Section 6 of the Agreement. Section 6.1 of the Agreement shall be deleted and replaced
with the following:

6.1 Good Standing and Compliance. Borrower and its Subsidiaries shall maintain all governmental
licenses, rights and agreements necessary for its operations or business and comply in all material
respects with all statutes, laws, ordinances and government rules and regulations to which it is
subject, except where the failure to do so would not reasonably be expected to result in a Material
Adverse Effect.

     V. Section 6 of the Agreement. Section 6.7 of the Agreement shall be deleted and replaced with
the following:

6.7 Taxes. Borrower and its Subsidiaries shall file all required tax returns, and shall pay all
taxes they owe other than where the failure to comply would not reasonably be expected to have a
Material Adverse Effect.

          VI. Section 6.10 of the Agreement shall be deleted and replaced with the following:

     6.10 Dissolution of Kior BV. Borrower shall not permit a Lien to arise on the capital stock
of Kior BV, or physically pledge the stock certificates of Kior BV, in favor of any other party
other than Lender and Borrower shall diligently pursue the dissolution of Kior BV as soon as
reasonably practicable. The Agent, on behalf of itself and the Lenders, hereby waives any Event of
Default that may have arisen under Section 8.3 of the Agreement as a result of the Borrower’s
inability to dissolve the existence of Kior BV prior to the date of this Amendment 2.

     VII. Section 6 of the Agreement. A new Section 6.11 and Section 6.12 shall be added:

6.11 Creation of Subsidiaries. Borrower shall provide Agent not less than 15 days prior written
notice of the formation of a Subsidiary after the date hereof, whether domestic or foreign. Except
as set forth herein, Borrower shall take all steps necessary at the request of Lenders to cause
each domestic Subsidiary to be a co-borrower hereunder or a guarantor hereof and shall cause such
Subsidiary to grant a first priority security interest in all of its assets to Agent on behalf of
Lenders and/or cause a pledge of such Subsidiary’s stock in favor of Agent on behalf of Lenders.
Borrower shall take all steps necessary at the request of Lenders to pledge in favor of Agent on
behalf of Lenders the capital stock of each foreign Subsidiary provided such pledge may be limited
to sixty-five percent (65%) of such Subsidiary’s capital stock. Notwithstanding the foregoing,
Columbus shall not be required to become a Borrower or guarantor hereof, and unless and until the
membership interests of Columbus are evidenced in
certificated form, Agent will not require a physical pledge of the membership interests of Columbus
(provided

 

 

nothing herein shall be deemed to release Agent’s security interest in such membership
interests). In addition, Agent agrees that from time to time in the future Borrower may form Exempt
Subsidiaries. Provided that Agent is given prior notice as required by the first sentence of this
Section 6.11, and provided such obligations are in form and substance acceptable to Agent, Borrower
shall not, upon Agent’s approval, be required to cause such Exempt Subsidiary to become a Borrower
or guarantor hereof, provided that nothing herein shall be deemed to release Agent’s security
interest in an Exempt Subsidiary’s capital stock or membership interests and Agent shall not be
deemed to have waived the right to request a physical pledge of such Exempt Subsidiary’s capital
stock in favor of Agent.

6.12 Issuance of New Warrants. On or before March 31, 2011, Borrower shall issue to each Lender a
New Warrant for the purchase of the Borrower’s Series C Preferred Stock in a total aggregate price
to all Lenders of $250,000, which series of preferred stock is to be authorized, designated, issued
and sold for purposes of an equity financing of Borrower after the date hereof in the amount of at
least $60,000,000 (the “Series C Offering”). In the event that the Series C Offering is not
completed by such date, then in such event, Borrower shall issue to each Lender a New Warrant for
the purchase of Borrower’s existing Series B Preferred Stock in a total aggregate price to all
Lenders of $250,000 with an exercise price of $9.84, and Borrower shall take all steps necessary to
authorize additional shares of Series B Preferred Stock (with identical terms, rights and
privileges as the authorized and issued Series B Preferred Stock) for issuance under the New
Warrant, including the amendment of Borrower’s Amended and Restated Certificate of Incorporation of
Kior, Inc. Borrower’s failure to issue and deliver the New Warrants to Lenders by March 31,
2011 shall be an Event of Default.

     VIII. Section 7 of the Agreement. Section 7.11 of the Agreement shall be deleted and replaced
with the following:

7.11 Deposit and Securities Accounts; Accounts of Exempt Subsidiaries. Maintain any deposit
accounts or accounts holding securities owned by Borrower except accounts in which Agent on behalf
of all Lenders has obtained a perfected first priority security interest. Notwithstanding the
foregoing, Lender shall not have a perfected security interest in (i) Borrower’s certificate of
deposit account no. 0910-00121407355 with Bank of America which secures Borrower’s commercial
credit card facility, provided the amount of such account shall not exceed $125,000; and (ii) any
deposit account maintained by Columbus, provided the amount of funds in such deposit account(s)
does not exceed at any time the sum of (a) $5,000,000 plus (b) the aggregate of the accounts
payable of Columbus then due and payable within the following 60 days; and (iii) any deposit
account maintained by an Exempt Subsidiary provided the amount of funds in such deposit account(s)
does not exceed at any time the sum of (a) $5,000,000 plus (b) the aggregate of the accounts
payable of such Exempt Subsidiary then due and payable within the following 60 days. For so long
as the Obligations are outstanding, Borrower shall not hold directly or indirectly, purchase or
create a purchase order or directive to purchase any auction rate securities or similar financial
instruments regardless of whether such securities are to be held by Borrower or through one or more
brokerage accounts.

     IX. Section 7 of the Agreement. Section 7.12 of the Agreement shall be deleted and replaced
with the following:

7.12 Maintenance of Subsidiaries. Except as set forth in Section 6.10 hereof Borrower shall not,
and shall not permit or cause any Subsidiary to, (i) except with respect to Columbus, and upon
Agent’s approval with respect to any future Exempt Subsidiary, which approval shall not be
unreasonably withheld and timely, sell, dispose of, convey, or allow a Lien to arise on any of its
assets, including Intellectual Property (as defined in Exhibit A) owned by such Subsidiary (and for
this purpose, the definition of “Intellectual Property” shall be deemed to refer to such
Subsidiary) except for non-exclusive licenses entered into in the ordinary course of business; (ii)
divest or “spin-off” any Subsidiary except where as a result of such transaction Borrower and/or
Borrower’s shareholders or affiliates retain or obtain majority ownership of such Subsidiary; (iii)
merge or consolidate any Subsidiary with or into another entity (unless as a result of such merger
Borrower and/or Borrower’s shareholders or affiliates retain or obtain majority ownership of the
surviving entity); (iv) permit a Change of Control (as defined below) of any Subsidiary; (v) make a
pledge of, any capital stock of any Subsidiary in favor of any person other than Lender; or (vi)
materially change the corporate structure and business operations of the Borrower and its
Subsidiaries taken as a whole. For
the purposes of this Section 7.12, a “Change of Control” shall mean, any transaction or series of

 

 

related transactions whereby the Borrower and/or Borrower’s shareholders or affiliates of Borrower
holding in excess of 50% of the outstanding voting capital stock of any Subsidiary immediately
prior to such transaction or transactions, shall own less than 50% of the outstanding voting or
capital stock of such Subsidiary immediately following such transaction or transactions.

     X. Conditions Precedent to the effectiveness of Amendment 2:

          The obligation of Lenders to enter into this Amendment 2 is subject to the performance and
fulfillment of each and every of the following conditions precedent in form and substance
satisfactory to Lenders in their sole discretion:

          (a) This Amendment 2 shall have been duly executed and delivered by Borrower.

          (b) The LCP Amended Note, the Leader-A Amended Note, and the Leader B Amended Note shall have
been duly executed and issued by Borrower to Lenders.

          (c) Without limiting the foregoing or Lender’s rights or Borrower’s Obligations under the
Agreement, such consents, including the approvals of Borrower’s board of directors, amendments,
filings, recordations, or other documents from any persons or entities necessary to maintain the
perfection and priority of Lenders’ security interest in the Collateral as amended hereby and as
originally configured, in form and substance satisfactory to Lenders in its sole discretion, shall
have been delivered by Borrower to Lenders.

          (d) A good standing certificate from Borrower’s state of incorporation or formation and the
state in which Borrower’s principal place of business is located, together with certificates of the
applicable governmental authorities stating that Borrower is in compliance with the franchise tax
laws of each such state, each dated as of a recent date shall have been delivered to Lenders.

          (e) All necessary consents of shareholders, members, and other third parties with respect to
the execution, delivery and performance of this Amendment 2, and the other Loan Documents shall
have been delivered to Lenders.

     XI. Additional Terms and Conditions

          (a) Further Conditions. The following are conditions precedent to Lenders’
obligations hereunder, without delivery and performance of which to Lenders’ satisfaction, the
original payment terms of the Loan Documents and the Notes shall remain in full force and effect,
unamended hereby:

               (i) Borrower shall deliver an Incumbency Certificate, in the form attached hereto as Exhibit
E-1, certified by responsible officers of Borrower, and attachments thereto including the
resolutions adopted by Borrower’s board of directors authorizing the execution and delivery of this
Amendment 2 and the other documents referred to in this Amendment 2 and the performance by Borrower
of its obligations under such documents.

               (ii) Borrower shall execute and deliver all other documents, as Lenders shall have reasonably
requested prior to the execution by Borrower and Lender of this Amendment 2.

          (b) Representations and Warranties of Borrower. Giving effect to this Amendment 2 and
the Disclosure Schedules attached hereto and made a part hereof, Borrower reaffirms the
representations and warranties made to Lenders in the Agreement as of the date hereof as though
fully set forth herein. Borrower further warrants and represents, as a significant material
inducement to Lenders to enter hereinto, that: (i) no Events of Default have occurred that have not
been disclosed to Lenders by Borrower in writing; (ii) it is not and has no reason to believe it
may be named as a party to any judicial or administrative proceeding, litigation or arbitration,
and has not received any communication from any person or entity (whether private or governmental)
threatening or indicating the same, except as previously disclosed to Lender in writing; and (iii)
it is in full compliance with Section 7.11 of the Agreement.

 

 

          (c) No Control. Borrower warrants and represents, as a significant material
inducement to Lenders to enter hereinto, that none of Lenders nor, to the Borrower’s knowledge, any
affiliate, officer, director, employee, agent, or attorney of Lenders, have at any time, from
Borrower’s date of formation through to the date hereof, (i) exercised management or other control
over the Borrower, (ii) exercised undue influence over Borrower or any of its officers, employees
or directors, (iii) made any representation or warranty, express or implied, to any party on behalf
of Borrower, (iv) entered into any joint venture, agency relationship, employment relationship, or
partnership with Borrower, (v) directed or instructed Borrower on the manner, method, amount, or
identity of payee of any payment made to any creditor of Borrower, and further, Borrower warrants
and represents that by entering hereinto with Lenders has not, are not and will not have engaged in
any of the foregoing.

          XI. Integration Clause. This Amendment 2, together with all Loan Documents required to be
entered into in connection with this Amendment 2, represents and documents the entirety of the
agreement and understanding of the parties hereto with respect to its subject matter. All prior
understandings, whether oral or written, other than the Loan Documents, are hereby merged hereinto.
NONE OF THE AGREEMENT OR THIS AMENDMENT 02 MAY BE MODIFIED EXCEPT BY A WRITING SIGNED BY LENDERS
AND BORROWER. Each provision hereof shall be severable from every other provision when determining
its legal enforceability such that Lenders’ rights and remedies under this Amendment 2 and the
Agreement may be enforced to the maximum extent permitted under applicable law. This Amendment 2
shall be binding upon, and inure to the benefit of, each party’s respective permitted successors
and assigns. This Amendment 2 may be executed in counterpart originals, all of which, when taken
together, shall constitute one and the same original document. No provision of any other document
between Lenders and Borrower shall limit the effectiveness hereof or the rights and remedies of
Lenders against Borrower.

 

 

Except as amended hereby, the Agreement remains unmodified and unchanged.

BORROWER:

Kior, Inc.

	 	 	 	 	 

	By:

	 	/s/ Fred Cannon	 	 
	Name:

	 	 

Fred Cannon
	 	 
	Title:

	 	President & CEO	 	 

AGENT:

	 	 	 	 	 

	Lighthouse Capital Partners VI, L.P.
	By:	 	Lighthouse Management Partners VI, L.L.C.,

its general partner
	 
	 	 	 	 
	By:
	 	 	 	 
	Name:

	 	 

	 	 
	Title:

	 	 

	 	 
	 

	 	 

	 	 

LENDERS:

	 	 	 	 	 	 	 	 	 

	Leader Lending, LLC — Series A	 	 	 	Leader Lending, LLC — Series B
	 
	 	 	 	 	 	 	 	 
	By:

	 	 	 	 	 	By:	 	 
	 

	 	 
	 	 	 	 	 	 
	Name:

	 	 	 	 	 	Name:	 	 
	 

	 	 
	 	 	 	 	 	 
	Title:

	 	 	 	 	 	Title:	 	 
	 

	 	 
	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Lighthouse Capital Partners VI, L.P.
	By:	 	Lighthouse Management Partners VI, L.L.C.,

its general partner
	 
	 	 	 	 	 	 	 	 
	By:
	 	 	 	 	 	 	 	 
	Name:

	 	 

	 	 	 	 	 	 
	Title:

	 	 

	 	 	 	 	 	 
	 

	 	 

	 	 	 	 	 	 

	 	 	 

	Attachments
	 	 
	 
	 	 
	Exhibit B-1

	 	Amended and Restated Promissory Note (Lighthouse)
	 
	 	 
	Exhibit B-2

	 	Amended and Restated Promissory Note (Leader — Series A)
	 
	 	 
	Exhibit B-3

	 	Amended and Restated Promissory Note (Leader — Series B)
	 
	 	 
	Exhibit C-2

	 	Form of New Warrant

 

 

	 	 	 

	Exhibit E-1

	 	Form of Incumbency Certificate
	 
	 	 
	Schedule 1-1

	 	Disclosure Schedule

 

 

Exhibit B-1

$4,124,449.66

Amended and Restated Secured Promissory Note 

This Amended and Restated Secured Promissory Note (this “Note”) is made effective
February 1, 2011, by Kior, Inc. (“Borrower”) in favor of Lighthouse Capital Partners
VI, L.P. (collectively with its assigns, “Lender”) and amends, restates and replaces in its
entirety that certain Secured Promissory Note dated January 29, 2010 in the principal amount of
$4,900,000, made by Borrower in favor of Lender pursuant to that certain Loan and Security
Agreement No. 1452 between Borrower, Lighthouse Capital Partners VI, L.P. as Agent, the other
lenders party thereto and Lender dated January 27, 2010 (the “Loan Agreement”). Initially
capitalized terms used and not otherwise defined herein shall have the meaning defined in the Loan
Agreement.

For Value Received, Borrower promises to pay in lawful money of the United States, to the
order of Lender, at 3555 Alameda de las Pulgas, Suite 200, Menlo Park, CA 94025, or such other
place as Lender may from time to time designate (“Lender’s Office”), the principal sum of
$4,124,449.66 (the “Advance”), including interest on the unpaid balance and all other amounts due
or to become due hereunder according to the terms hereof and of the Loan Agreement.

“Amendment Fee” means $175,000; $35,000 of which has been paid as of the date hereof; the remaining
$140,000 of which shall be due and payable on the Maturity Date.

“Basic Rate” a per annum rate of interest equal to (i) 13% during the Interest Only Period and (ii)
12% on and after the Loan Commencement Date.

“Final Payment” means $367,500.

“Interest Only Period” means the period commencing on February 1, 2011 and continuing through the
day immediately preceding the Loan Commencement Date.

“Loan Commencement Date” means March 1, 2012.

“Maturity Date” means the last day of the Repayment Period, or if earlier, the date of prepayment
under the Note.

“Payment Date” means the first day of each calendar month.

“Prepayment Fee” means (i) 3% of the outstanding principal amount being prepaid for any prepayment
made on or before December 31, 2011; (ii) 2% of the outstanding principal amount being prepaid for
any prepayment made during calendar year 2012; and (iii) 1% of the outstanding principal amount
being prepaid for any prepayment made during calendar year 2013 or thereafter.

“Repayment Period” means the period beginning on the Loan Commencement Date and continuing for 24
calendar months.

1. Repayment. Borrower shall pay principal and interest due hereunder from the Funding Date, until
this Note is paid in full, on each Payment Date pursuant to the terms of the Loan Agreement and
this Note. Prior to the Loan Commencement Date, Borrower shall pay to Lender, monthly in advance
on each Payment Date, interest calculated using the Basic Rate. Beginning on the Loan Commencement
Date and on each Payment Date thereafter during the Repayment Period, Borrower shall make equal
installments of principal and interest in advance, calculated at the Basic Rate. On the Maturity
Date, Borrower shall pay, in addition to all unpaid principal and interest outstanding hereunder,
the Final Payment and the Amendment Fee.

2. Interest. Interest not paid when due will, to the maximum extent permitted under applicable
law, become part of principal, at Lender’s option, and thereafter bear like interest as principal.
All interest computation shall be

 

 

based on a 360-day year and actual days elapsed prior to the Loan Commencement Date and on a
360-day year and 30 day month on and after the Loan Commencement Date. All Obligations not paid
when due shall bear interest at the Default Rate unless waived in writing by Lender. All amounts
paid hereunder will be applied to the Obligations in Lender’s discretion and as provided in the
Loan Agreement.

3. Voluntary Prepayment. Borrower may prepay the Note if and only if Borrower pays to Lender (i)
the outstanding principal amount of this Note and any unpaid accrued interest; (ii) the Final
Payment; (iii) the Prepayment Fee, if applicable; (iv) the Amendment Fee; and (v) all other sums,
if any, that shall have become due and payable hereunder with respect to this Note.

4. Collateral. This Note is secured by the Collateral.

5. Waivers. Borrower, and all guarantors and endorsers of this Note, regardless of the time, order
or place of signing, hereby waive notice, demand, presentment, protest, and notices of every kind,
presentment for the purpose of accelerating maturity, diligence in collection, and, to the fullest
extent permitted by law, all rights to plead any statute of limitations as a defense to any action
on this Note.

6. Choice of Law; Venue. This Note shall be governed by, and construed in accordance with the
internal laws of the State of California, without regard to principles of conflicts of law. Each
of Borrower and Lender hereby submits to the exclusive jurisdiction and venue of the State and
Federal courts located in the City and County of San Francisco, State of California. Borrower and
Lender each hereby waive their respective rights to a jury trial of any claim or cause of action
based upon or arising out of this Note. Each party further waives any right to consolidate any
action in which a jury trial has been waived with any other action in which a jury trial cannot be
or has not been waived.

7. Miscellaneous. This Note may be modified only by a writing signed by Borrower and
Lender. Each provision hereof is severable from every other provision hereof and of the Loan
Agreement when determining its legal enforceability. Sections and subsections are titled for
convenience, and not for construction. “Hereof,” “herein,” “hereunder,” and similar words refer to
this Note in its entirety. “Or” is not necessarily exclusive. “Including” is not limiting. The
terms and conditions hereof inure to the benefit of and are binding upon the parties’ respective
permitted successors and assigns. This Note is subject to all the terms and conditions of the Loan
Agreement.

In Witness Whereof, Borrower has caused this Note to be executed by a duly authorized
officer as of the day and year first above written.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

Fred Cannon
	 	 
	 

	 	Title:
	 	President & CEO	 	 

 

 

Exhibit B-2

$883,810.64

Amended and Restated Secured Promissory Note 

This Amended and Restated Secured Promissory Note (this “Note”) is made effective
February 1, 2011, by Kior, Inc. (“Borrower”) in favor of Leader Lending, LLC —
Series A (collectively with its assigns, “Lender”) and amends, restates and replaces in its
entirety that certain Secured Promissory Note dated January 29, 2010 in the principal amount of
$1,050,000, made by Borrower in favor of Lender pursuant to that certain Loan and Security
Agreement No. 1452 between Borrower, Lighthouse Capital Partners VI, L.P. as Agent, the other
lenders party thereto and Lender dated January 27, 2010 (the “Loan Agreement”). Initially
capitalized terms used and not otherwise defined herein shall have the meaning defined in the Loan
Agreement.

For Value Received, Borrower promises to pay in lawful money of the United States, to the
order of Lender, at 311 California Street, Suite 420, San Francisco, CA 94104, or such other place
as Lender may from time to time designate (“Lender’s Office”), the principal sum of $883,810.64
(the “Advance”), including interest on the unpaid balance and all other amounts due or to become
due hereunder according to the terms hereof and of the Loan Agreement.

“Amendment Fee” means $37,500; $7,500 of which has been paid as of the date hereof; the remaining
$30,000 of which shall be due and payable on the Maturity Date.

“Basic Rate” a per annum rate of interest equal to (i) 13% during the Interest Only Period and (ii)
12% on and after the Loan Commencement Date.

“Final Payment” means $78,750.

“Interest Only Period” means the period commencing on February 1, 2011 and continuing through the
day immediately preceding the Loan Commencement Date.

“Loan Commencement Date” means March 1, 2012.

“Maturity Date” means the last day of the Repayment Period, or if earlier, the date of prepayment
under the Note.

“Payment Date” means the first day of each calendar month.

“Prepayment Fee” means (i) 3% of the outstanding principal amount being prepaid for any prepayment
made on or before December 31, 2011; (ii) 2% of the outstanding principal amount being prepaid for
any prepayment made during calendar year 2012; and (iii) 1% of the outstanding principal amount
being prepaid for any prepayment made during calendar year 2013 or thereafter.

“Repayment Period” means the period beginning on the Loan Commencement Date and continuing for 24
calendar months.

1. Repayment. Borrower shall pay principal and interest due hereunder from the Funding Date, until
this Note is paid in full, on each Payment Date pursuant to the terms of the Loan Agreement and
this Note. Prior to the Loan Commencement Date, Borrower shall pay to Lender, monthly in advance
on each Payment Date, interest calculated using the Basic Rate. Beginning on the Loan Commencement
Date and on each Payment Date thereafter during the Repayment Period, Borrower shall make equal
installments of principal and interest in advance, calculated at the Basic Rate. On the Maturity
Date, Borrower shall pay, in addition to all unpaid principal and interest outstanding hereunder,
the Final Payment and the Amendment Fee.

2. Interest. Interest not paid when due will, to the maximum extent permitted under applicable
law, become part of principal, at Lender’s option, and thereafter bear like interest as principal.
All interest computation shall be

 

 

based on a 360-day year and actual days elapsed prior to the Loan Commencement Date and on a
360-day year and 30 day month on and after the Loan Commencement Date. All Obligations not paid
when due shall bear interest at the Default Rate unless waived in writing by Lender. All amounts
paid hereunder will be applied to the Obligations in Lender’s discretion and as provided in the
Loan Agreement.

3. Voluntary Prepayment. Borrower may prepay the Note if and only if Borrower pays to Lender (i)
the outstanding principal amount of this Note and any unpaid accrued interest; (ii) the Final
Payment; (iii) the Prepayment Fee, if applicable; (iv) the Amendment Fee; and (v) all other sums,
if any, that shall have become due and payable hereunder with respect to this Note.

4. Collateral. This Note is secured by the Collateral.

5. Waivers. Borrower, and all guarantors and endorsers of this Note, regardless of the time, order
or place of signing, hereby waive notice, demand, presentment, protest, and notices of every kind,
presentment for the purpose of accelerating maturity, diligence in collection, and, to the fullest
extent permitted by law, all rights to plead any statute of limitations as a defense to any action
on this Note.

6. Choice of Law; Venue. This Note shall be governed by, and construed in accordance with the
internal laws of the State of California, without regard to principles of conflicts of law. Each
of Borrower and Lender hereby submits to the exclusive jurisdiction and venue of the State and
Federal courts located in the City and County of San Francisco, State of California. Borrower and
Lender each hereby waive their respective rights to a jury trial of any claim or cause of action
based upon or arising out of this Note. Each party further waives any right to consolidate any
action in which a jury trial has been waived with any other action in which a jury trial cannot be
or has not been waived.

7. Miscellaneous. This Note may be modified only by a writing signed by Borrower and
Lender. Each provision hereof is severable from every other provision hereof and of the Loan
Agreement when determining its legal enforceability. Sections and subsections are titled for
convenience, and not for construction. “Hereof,” “herein,” “hereunder,” and similar words refer to
this Note in its entirety. “Or” is not necessarily exclusive. “Including” is not limiting. The
terms and conditions hereof inure to the benefit of and are binding upon the parties’ respective
permitted successors and assigns. This Note is subject to all the terms and conditions of the Loan
Agreement.

In Witness Whereof, Borrower has caused this Note to be executed by a duly authorized
officer as of the day and year first above written.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

Fred Cannon
	 	 
	 

	 	Title:
	 	President & CEO	 	 

 

 

Exhibit B-3

$883,810.64

Amended and Restated Secured Promissory Note 

This Amended and Restated Secured Promissory Note (this “Note”) is made effective
February 1, 2011, by Kior, Inc. (“Borrower”) in favor of Leader Lending, LLC —
Series B (collectively with its assigns, “Lender”) and amends, restates and replaces in its
entirety that certain Secured Promissory Note dated January 29, 2010 in the principal amount of
$1,050,000, made by Borrower in favor of Lender pursuant to that certain Loan and Security
Agreement No. 1452 between Borrower, Lighthouse Capital Partners VI, L.P. as Agent, the other
lenders party thereto and Lender dated January 27, 2010 (the “Loan Agreement”). Initially
capitalized terms used and not otherwise defined herein shall have the meaning defined in the Loan
Agreement.

For Value Received, Borrower promises to pay in lawful money of the United States, to the
order of Lender, at 311 California Street, Suite 420, San Francisco, CA 94104, or such other place
as Lender may from time to time designate (“Lender’s Office”), the principal sum of $883,810.64
(the “Advance”), including interest on the unpaid balance and all other amounts due or to become
due hereunder according to the terms hereof and of the Loan Agreement.

“Amendment Fee” means $37,500; $7,500 of which has been paid as of the date hereof; the remaining
$30,000 of which shall be due and payable on the Maturity Date.

“Basic Rate” a per annum rate of interest equal to (i) 13% during the Interest Only Period and (ii)
12% on and after the Loan Commencement Date.

“Final Payment” means $78,750.

“Interest Only Period” means the period commencing on February 1, 2011 and continuing through the
day immediately preceding the Loan Commencement Date.

“Loan Commencement Date” means March 1, 2012.

“Maturity Date” means the last day of the Repayment Period, or if earlier, the date of prepayment
under the Note.

“Payment Date” means the first day of each calendar month.

“Prepayment Fee” means (i) 3% of the outstanding principal amount being prepaid for any prepayment
made on or before December 31, 2011; (ii) 2% of the outstanding principal amount being prepaid for
any prepayment made during calendar year 2012; and (iii) 1% of the outstanding principal amount
being prepaid for any prepayment made during calendar year 2013 or thereafter.

“Repayment Period” means the period beginning on the Loan Commencement Date and continuing for 24
calendar months.

1. Repayment. Borrower shall pay principal and interest due hereunder from the Funding Date, until
this Note is paid in full, on each Payment Date pursuant to the terms of the Loan Agreement and
this Note. Prior to the Loan Commencement Date, Borrower shall pay to Lender, monthly in advance
on each Payment Date, interest calculated using the Basic Rate. Beginning on the Loan Commencement
Date and on each Payment Date thereafter during the Repayment Period, Borrower shall make equal
installments of principal and interest in advance, calculated at the Basic Rate. On the Maturity
Date, Borrower shall pay, in addition to all unpaid principal and interest outstanding hereunder,
the Final Payment and the Amendment Fee.

2. Interest. Interest not paid when due will, to the maximum extent permitted under applicable
law, become part of principal, at Lender’s option, and thereafter bear like interest as principal.
All interest computation shall be

 

 

based on a 360-day year and actual days elapsed prior to the Loan Commencement Date and on a
360-day year and 30 day month on and after the Loan Commencement Date. All Obligations not paid
when due shall bear interest at the Default Rate unless waived in writing by Lender. All amounts
paid hereunder will be applied to the Obligations in Lender’s discretion and as provided in the
Loan Agreement.

3. Voluntary Prepayment. Borrower may prepay the Note if and only if Borrower pays to Lender (i)
the outstanding principal amount of this Note and any unpaid accrued interest; (ii) the Final
Payment; (iii) the Prepayment Fee, if applicable; (iv) the Amendment Fee; and (v) all other sums,
if any, that shall have become due and payable hereunder with respect to this Note.

4. Collateral. This Note is secured by the Collateral.

5. Waivers. Borrower, and all guarantors and endorsers of this Note, regardless of the time, order
or place of signing, hereby waive notice, demand, presentment, protest, and notices of every kind,
presentment for the purpose of accelerating maturity, diligence in collection, and, to the fullest
extent permitted by law, all rights to plead any statute of limitations as a defense to any action
on this Note.

6. Choice of Law; Venue. This Note shall be governed by, and construed in accordance with the
internal laws of the State of California, without regard to principles of conflicts of law. Each
of Borrower and Lender hereby submits to the exclusive jurisdiction and venue of the State and
Federal courts located in the City and County of San Francisco, State of California. Borrower and
Lender each hereby waive their respective rights to a jury trial of any claim or cause of action
based upon or arising out of this Note. Each party further waives any right to consolidate any
action in which a jury trial has been waived with any other action in which a jury trial cannot be
or has not been waived.

7. Miscellaneous. This Note may be modified only by a writing signed by Borrower and
Lender. Each provision hereof is severable from every other provision hereof and of the Loan
Agreement when determining its legal enforceability. Sections and subsections are titled for
convenience, and not for construction. “Hereof,” “herein,” “hereunder,” and similar words refer to
this Note in its entirety. “Or” is not necessarily exclusive. “Including” is not limiting. The
terms and conditions hereof inure to the benefit of and are binding upon the parties’ respective
permitted successors and assigns. This Note is subject to all the terms and conditions of the Loan
Agreement.

In Witness Whereof, Borrower has caused this Note to be executed by a duly authorized
officer as of the day and year first above written.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

Fred Cannon
	 	 
	 

	 	Title:
	 	President & CEO	 	 

 

 

Exhibit E-1

Incumbency Certificate

     The undersigned, Andre Ditsch, hereby certifies that:

1. He/She is the duly elected and acting Secretary of Kior, Inc., a Delaware corporation
(the “Company”).

2. That on the date hereof, each person listed below holds the office in the Company indicated
opposite his or her name and that the signature appearing thereon is the genuine signature of each
such person:

	 	 	 	 	 
	NAME	 	OFFICE	 	SIGNATURE
	 
	 	 	 	 
	Fred Cannon

	 	President & Chief Operating

Officer
	 	 

	 
	 	 	 	 
	John H. Karnes

	 	Chief Financial Officer
	 	 

	 
	 	 	 	 
	Andre Ditsch

	 	Secretary
	 	 

3. Attached hereto as Exhibit A is a true and correct copy of the Certificate of Incorporation of
the Company, as amended, as in effect as of the date hereof.

4. Attached hereto as Exhibit B is a true and correct copy of the Bylaws of the Company, as
amended, as in effect as of the date hereof.

5. Attached hereto as Exhibit C is a copy of the resolutions of the Board of Directors of the
Company authorizing and approving the Company’s execution, delivery and performance of an amendment
to the loan facility with Lighthouse Capital Partners VI, L.P.

     IN WITNESS WHEREOF, the undersigned has executed this Incumbency Certificate on February 28,
2011.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

Andre Ditsch
	 	 
	 

	 	Title:
	 	Secretary	 	 

     I, the President and Chief Operating Officer of the Company, do hereby certify that Andre
Ditsch is the duly qualified, elected and acting Secretary of the Company and that the above
signature is his or her genuine signature.

     IN WITNESS WHEREOF, the undersigned has executed and delivered this Incumbency Certificate on
February 28, 2011.

	 	 	 	 	 	 	 

	 	 	Kior, Inc.	 	 
	 
	 	 	 	 	 	 
	 

	 	By:	 	 	 	 
	 

	 	Name:
	 	 

Fred Cannon
	 	 
	 

	 	Title:
	 	President and Chief Operating Officer	 	 

 

 

Schedule 1-1

Disclosure Schedule

Deposit and Securities Accounts

	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	LCP
	 	 	 	 	 	 	 	 	 	 	Office
	 	 	 	 	 	 	Contact Information for	 	Use
	 	 	Account Information:	 	Account:	 	Only:
	Account
	 	Bank Name:	 	Silicon Valley Bank	 	Contact Name:	 	Cynthia Brooks-Manson	 	ACA
	Number
	 	Address:	 	3005 Tasman Drive	 	Phone:	 	(512) 372-6763	 	X
	1
	 	City, State, Zip:	 	Santa Clara, CA 95054	 	Fax:	 	(512) 346-9207	 	 
	(ACH Account)
	 	Phone:	 	(408) 654-7400	 	E-mail:	 	cbrooks@svb.com	 	 
	 
	 	Fax:	 	 	 	 	 	 	 	 
	 
	 	Type of Account:	 	Checking — KiOR, Inc.	 	 	 	 	 	 
	 
	 	Account number:	 	3300709708	 	 	 	 	 	 
	 
	 	Approx Balance	 	$1,100,000 @ 2/6/2011	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Account Number
	 	Bank Name:	 	Silicon Valley Bank / US Bank	 	Contact Name:	 	Cynthia Brooks-Manson	 	ACA
	2
	 	Address:	 	3005 Tasman Drive	 	Phone:	 	(512) 372-6763	 	 No
	(Money Market
	 	City, State, Zip:	 	Santa Clara, CA 95054	 	Fax:	 	(512) 346-9207	 	 
	Account)
	 	Phone:	 	(408) 654-7400	 	E-mail:	 	cbrooks@svb.com	 	 
	 
	 	Fax:	 	 	 	 	 	 	 	 
	 
	 	Type of Account:	 	Custodial Account	 	 	 	 	 	 
	 
	 	Account number:	 	19-SV613 — KiOR, Inc	 	 	 	 	 	 
	 
	 	Approx Balance	 	$35,000,000	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Account Number
	 	Bank Name:	 	Bank of America	 	Contact Name:	 	Tim Thurman	 	ACA
	3
	 	Address:	 	12400 I 45 North Freeway	 	Phone:	 	(888) 852-5000, ex 5640	 	No
	 
	 	City, State, Zip:	 	Houston, TX 77060	 	Fax:	 	(800) 839-9516	 	 
	 
	 	Phone:	 	 	 	E-mail:	 	timothy.thurman@baml.com	 	 
	 
	 	Fax:	 	 	 	 	 	 	 	 
	 
	 	Type of Account:	 	Certificate of Deposit  — 	 	 	 	 	 	 
	 
	 	 	 	KiOR, Inc.	 	 	 	 	 	 
	 
	 	Account number:	 	0910-00121407355	 	 	 	 	 	 
	 
	 	(support for credit card)	 	 	 	 	 
	 
	 	Approx Balance	 	$102,000	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Account Number
	 	Bank Name:	 	Silicon Valley Bank	 	Contact Name:	 	Cynthia Brooks-Manson	 	ACA
	4
	 	Address:	 	3005 Tasman Drive	 	Phone:	 	(512) 372-6763	 	X
	 
	 	City, State, Zip:	 	Santa Clara, CA 95054	 	Fax:	 	(512) 346-9207	 	 
	 
	 	Phone:	 	(408) 654-7400	 	E-mail:	 	cbrooks@svb.com	 	 
	 
	 	Fax:	 	 	 	 	 	 	 	 
	 
	 	Type of Account:	 	Checking — KiOR Columbus	 	 	 	 	 	 
	 
	 	Account number:	 	3300765426	 	 	 	 	 	 
	 
	 	Approx Balance	 	$5,00,000 @ 2/6/2011	 	 	 	 	 	 

Permitted Liens

Existing Liens: 

 

 

	 	•	 	Lien of Lighthouse Capital Partners VI, L.P. securing obligations of Parent under that
certain Loan and Security Agreements No. 1451 & 1452 dated December 30, 2008 and January
27, 2010 respectively.
	 
	 	•	 	Operating Leases as outlined below:

	 	 	 	 	 
	Vendor	 	Property Description	 	Dates Covered
	Great America

	 	Konica Minolta C351 Full Color Copier
	 	6/9/09-6/9/12
	Great America

	 	Konica Minolta Bizhub digital copier (used)
	 	8/25/08-8/24/11
	Great America

	 	Konica Minolta Bizhub 350 Copier System
	 	3/10/10 — 3/10/13
	Great America

	 	Konica Minolta Bizhub digital copier (used)
	 	9/14/10 — 9/14/13
	CPM LABFAB Inc.

	 	One Lab
	 	11/1/08-11/1/10
	CPM LABFAB Inc.

	 	Two Labs
	 	12/1/08-12/1/10
	CPM LABFAB Inc.

	 	One Lab
	 	6/1/10 — 6/1/11
	Southern Ionics Inc.

	 	Plant Site
	 	11/1/08-10/31/11
	De Lage Landen

	 	Forklift
	 	9/1/09 — 9/1/12
	Mobile Modular

	 	Offices — Contract 230000644.1
	 	12/1/08-12/1/11
	Mobile Modular

	 	Offices — Contract 230000120.1
	 	12/7/08 — 12/7/11
	Mobile Modular

	 	Offices — Contract 230000329.1
	 	5/7/09 — 5/7/12
	Mobile Modular

	 	Offices — Contract 230001286.1
	 	10/1/10 — 10/1/13
	Quantum Analytics

	 	Pyrolyzer
	 	8/7/10 — 8/7/13
	Quantum Analytics

	 	Pyrolyzer
	 	11/5/10 — 11/5/13

Subsidiaries

Kior BV in liquidation, a wholly owned subsidiary of Borrower organized under the laws of The
Netherlands.

Kior Columbus LLC, a limited liability company organized under the laws of Delaware and a
wholly-owned subsidiary of Parent.

Prior Names

Bio Catalytic Cracking, Inc.

5.6 Litigation and Administrative Proceedings

Parent has initiated a lawsuit against George Huber (“Huber”), a prior member of the Borrower’s
scientific advisory board, based in part on a belief that Huber may have breached the terms of his
consulting agreement with Borrower.

A former employee has instituted summary proceedings against Kior BV in Dutch courts claiming
continuation of employment even though his employment contract ended April 30, 2010.

5.15 KIOR BV

Kior BV currently holds almost no cash reserves. Kior BV is a party to no agreements other than an
intercompany agreement between Kior, Inc. and Kior BV.

Hans Heinerman was the sole employee of Kior BV and his employment was terminated prior to April
30, 2010. A final severance agreement with Mr. Heinerman has not been completed due to ongoing
court proceedings in the Netherlands and is holding up final liquidation of Kior BV.

 

 

Business Premises

	 	 	 	 	 	 	 	 	 
	 	 	Each Location Address where Lighthouse	 	Landlord/Property Management
	 	 	Capital Partners has financed assets:	 	Information:
	Current
	 	Contact Name:	 	G. E. Staggs	 	Contact Name:	 	Milton  Sundbeck,
	Headquarters
	 	Address:	 	13001 Bay Park Road	 	 	 	President
	(Location 1)
	 	City, State, Zip:	 	Pasadena, TX 77507	 	Company Name:	 	Southern Ionics
	 
	 	Phone:	 	(281) 694-8710	 		 	Incorporated
	 
	 	Fax:	 	(281) 694-8799	 	Address:	 	Drawer 1217
	 
	 	 	 	 	 	City, State, Zip:	 	West Point, MS 39701
	 
	 	 	 	 	 	Phone:	 	(662) 494-3055 x 201
	 
	 	 	 	 	 	Fax:	 	(662) 495-2590
	 
	 	 	 	 	 	Local Contact:	 	Craig Cantrell,
	 
	 	 	 	 	 	 	 	Plant Manager
	 
	 	 	 	 	 	Local Address:	 	12901 Baypark Rd.
	 
	 	 	 	 	 	City, State, Zip:	 	Pasadena, TX 77507
	 
	 	 	 	 	 	Phone:	 	(281) 474-4826 x 131
	 
	 	 	 	 	 	Cell:	 	(281) 703-3439
	 
	 	 	 	 	 	Fax:	 	(281) 474-4973exv10w6

Exhibit 10.6

KIOR, Inc.

Nonstatutory Stock Option Agreement

Granted Under Amended and Restated 2007 Stock Option/ Stock Issuance Plan

1. Grant of Option.

     This agreement evidences the grant by Kior, Inc., a Delaware corporation (the “Company”), on
March 18, 2011 (the “Grant Date”) to [________], an employee of the Company (the “Participant”), of
an option to purchase, in whole or in part, on the terms provided herein and in the Company’s
Amended and Restated 2007 Stock Option/ Stock Issuance Plan (the “Plan”), a total of [________]
shares of Class A common stock, $0.0001 par value per share, of the Company (the “Common Stock”) at
$3.96 per share. Unless earlier terminated, this option shall expire at 5:00 p.m., Central Time,
on December 31, 2016 (the “Final Exercise Date”).

     It is intended that the option evidenced by this agreement shall not be an incentive stock
option as defined in Section 422 of the Internal Revenue Code of 1986, as amended, and any
regulations promulgated thereunder (the “Code”). Except as otherwise indicated by the context, the
term “Participant”, as used in this option, shall be deemed to include any person who acquires the
right to exercise this option validly under its terms. All capitalized terms not defined herein
shall have the meaning assigned to such term under the Plan.

2. Vesting Schedule.

     (a) This option will vest as to 100% of the total number of option shares on the fifth
anniversary of the Grant Date. Except as set forth below in Sections 2(b) and 2(c), to the extent
that the Participant terminates employment for any reason or no reason prior to the vesting of the
option, the option shall terminate and be of no further force or effect.

     (b) In the event of the death or Disability of the Participant between the Grant Date and
March 18, 2016, a number of the option shares shall immediately become vested shares, calculated by
multiplying the total number of option shares by a fraction, the numerator of which is equal to the
number of days elapsed between the Grant Date and the date of such death or Disability and the
denominator of which is the total number of days between the Grant Date and March 18,2016;
provided, however, that if the Participant’s death or Disability occurs prior to March 18, 2012, no
vesting of the option shall occur as a result of such event. For purposes of this agreement,
“Disability” shall have the meaning set forth in Treasury Regulation 1.409A-3(i)(4).

     (c) In the event of the tennination of the Participant’s employment without Cause (as defined
in such Participant’s employment agreement with the Company) or resignation from employment by the
Participant for Good Reason (as defined such Participant’s employment greement with the Company) in
the 12 months following a Change of Control (as defined in the Plan), all option shares shall
immediately become vested shares.

 

 

3. Exercise of Option.

     (a) Form of Exercise. An election to exercise this option shall be in writing, signed
by the Participant, and received by the Company at its principal office, accompanied by this
agreement, and payment in full in the manner provided in the Plan. The Participant may purchase
less than the number of Common Stock covered hereby, provided that no partial exercise of this
option may be for any fractional share of Common Stock.

     (b) Time of Exercise. This option may only be exercised on the earlier of (i) the
first business day after the date thirty (30) days after the first date on which the Participant is
separated from service (determined as described below) from the Company; (ii) the first business
day after the date sixty (60) days after the date of the Participant’s death; or (iii) the first
business day after the date sixty (60) days after the Participant’s Disability (the earlier of the
dates set forth in subsections (i), (ii) and (iii) being referred to as the “Required Exercise
Date”), provided that this option shall be exercisable only with respect to the portion of the
option that has vested on the date of Participant’s separation from service, death or Disability,
as the case may be; and the option shall terminate at such time with respect to any unvested
portion of the option. Notwithstanding the foregoing, if the Required Exercise Date does not occur
prior to November 1, 2016, then this option may also be exercised at any time between November 1,
2016 and the earlier of the Required Exercise Date and December 31, 2016. This option may not be
exercised on more than one occasion or after the earlier of the Required Exercise Date and the
Final Exercise Date.

     (c) Changes in Exercise Dates. Neither the Company nor the Participant shall have the
right to accelerate or defer any exercise date or payment date except to the extent specifically
permitted or required by Section 409A of the Code.

     (d) Separation From Service. The determination of whether and when a separation from
service from the Company has occurred shall be made and in a manner consistent with, and based on
the presumptions set forth in, Treasury Regulation Section 1.409A-1(h). Solely for purposes of
this Section 3(d), “Company” shall include all persons with whom the Company would be considered a
single employer as determined under Treasury Regulation Section 1.409A-1(h)(3).

     (e) Special Rule for Specified Employees. If, as of the date of the Participant’s
“separation from service” from the Company, the Participant is a “specified employee” (within the
meaning of Section 409A of the Code) and pursuant to Section 3(b) above the Participant would
otherwise be permitted to exercise this option within the six-month period following the date of
the Participant’s “separation from service” from the Company, then the first permitted exercise
date shall instead be the date that is six months and one day after such date of separation from
service (or, if earlier, sixty (60) days after the Participant’s death).

     (f) Certain Transactions. To the extent that the option is (i) adjusted pursuant to
Article One, Section V.C. of the Plan or (ii) assumed by a successor corporation pursuant to
Article Two, Section III. of the Plan, such adjustment or assumption, as the case may be,
shall be undertaken in a manner that complies with Section 409A of the Code.

-2-

 

4. Company Right of First Refusal

     (a) Notice of Proposed Transfer. If the Participant proposes to sell, assign,
transfer, pledge, hypothecate or otherwise dispose of, by operation of law or otherwise
(collectively, “transfer”) any Common Stock acquired upon exercise of this option, then the
Participant shall first give written notice of the proposed transfer (the “Transfer Notice”) to the
Company. The Transfer Notice shall name the proposed transferee and state the number of shares of
Common Stock the Participant proposes to transfer (the “Offered Common Stock”), the price per share
and all other material terms and conditions of the transfer.

     (b) Company Right to Purchase. For 30 days following its receipt of such Transfer
Notice, the Company shall have the option to purchase all or part of the Offered Common Stock at
the price and upon the terms set forth in the Transfer Notice. In the event the Company elects to
purchase all or part of the Offered Common Stock, it shall give written notice of such election to
the Participant within such 30-day period. Within 10 days after his or her receipt of such notice,
the Participant shall tender to the Company at its principal offices the certificate or
certificates representing the Offered Shares to be purchased by the Company, duly endorsed in blank
by the Participant or with duly endorsed stock powers attached thereto, all in a form suitable for
transfer of the Offered Shares to the Company. Promptly following receipt of such certificate or
certificates, the Company shall deliver or mail to the Participant a check in payment of the
purchase price for such Offered Shares; provided that if the terms of payment set
forth in the Transfer Notice were other than cash against delivery, the Company may pay for the
Offered Shares on the same terms and conditions as were set forth in the Transfer Notice; and
provided further that any delay in making such payment shall not invalidate the
Company’s exercise of its option to purchase the Offered Shares.

     (c) Common Stock Not Purchased By Company. If the Company does not elect to acquire
all of the Offered Common Stock, the Participant may, within the 30-day period following the
expiration of the option granted to the Company under subsection (b) above, transfer the Offered
Common stock which the Company has not elected to acquire to the proposed transferee,
provided that such transfer shall not be on terms and conditions more favorable to
the transferee than those contained in the Transfer Notice. Notwithstanding any of the above, all
Offered Common Stock transferred pursuant to this Section 4 shall remain subject to the right of
first refusal set forth in this Section 4 and such transferee shall, as a condition to such
transfer, deliver to the Company a written instrument confirming that such transferee shall be
bound by all of the terms and conditions of this Section 4.

     (d) Consequences of Non-Delivery. After the time at which the Offered Common Stock is
required to be delivered to the Company for transfer to the Company pursuant to subsection (b)
above, the Company shall not pay any dividend to the Participant on account of such Offered Common
Stock or permit the Participant to exercise any of the privileges or rights of a stockholder with
respect to such Offered Common Stock, but shall, insofar as permitted by law, treat the Company as
the owner of such Offered Common Stock.

     (e) Exempt Transactions. The following transactions shall be exempt from the
provisions of this Section 4:

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          (1) any transfer of Common Stock to or for the benefit of any spouse, child or grandchild of
the Participant, or to a trust for their benefit;

          (2) any transfer pursuant to an effective registration statement filed by the Company under
the Securities Act of 1933, as amended (the “Securities Act”); and

          (3) the sale of all or substantially all of the outstanding shares of capital stock of the
Company (including pursuant to a merger or consolidation);

provided, however, that in the case of a transfer pursuant to clause (1) above,
such Common Stock shall remain subject to the right of first refusal set forth in this Section 4.

     (f) Assignment of Company Right. The Company may assign its rights to purchase
Offered Common Stock in any particular transaction under this Section 4 to one or more persons or
entities.

     (g) Termination. The provisions of this Section 4 shall terminate upon the earlier of
the following events:

          (1) the closing of the sale of shares of Common Stock in an underwritten public offering
pursuant to an effective registration statement filed by the Company under the Securities Act; or

          (2) the sale of all or substantially all of the outstanding shares of capital stock, assets or
business of the Company, by merger, consolidation, sale of assets or otherwise (other than a merger
or consolidation in which all or substantially all of the individuals and entities who were
beneficial owners of the Company’s voting securities immediately prior to such transaction
beneficially own, directly or indirectly, more than 75% (determined on an as-converted basis) of
the outstanding securities entitled to vote generally in the election of directors of the
resulting, surviving or acquiring corporation in such transaction).

     (h) No Obligation to Recognize Invalid Transfer. The Company shall not be required
(1) to transfer on its books any of the Common Stock which shall have been sold or transferred in
violation of any of the provisions set forth in this Section 4, or (2) to treat as owner of such
Common Stock or to pay dividends to any transferee to whom any such Common Stock shall have been so
sold or transferred.

5. Agreement in Connection with Initial Public Offering.

     The Participant agrees, in connection with the initial underwritten public offering of the
Common Stock on a recognized stock exchange, (i) not to (a) offer, pledge, announce the intention
to sell, sell, contract to sell, sell any option or contract to purchase, purchase any option or
contract to sell, grant any option, right or warrant to purchase, or otherwise transfer or dispose
of, directly or indirectly, any shares of Common Stock or any other securities of the Company or
(b) enter into any swap or other agreement that transfers, in whole or in part, any of the economic
consequences of ownership of shares of Common Stock or other securities of the Company, whether any
transaction described in clause (a) or (b) is to be settled by delivery of securities, in cash or
otherwise, during the period beginning on the date of the filing of the final prospectus

-4-

 

relating
to the offering and ending 180 days after the date of the final prospectus relating to the offering
or such period as advised by the managing underwriters for such offering, and (ii) to execute any
agreement reflecting clause (i) above as may be requested by the Company or the managing
underwriters at the time of such offering. The Company may impose stop-transfer instructions with
respect to the shares of Common Stock or other securities subject to the foregoing restriction
until the end of the “lock-up” period.

6. Withholding.

     No Common Stock will be issued pursuant to the exercise of this option unless and until the
Participant pays to the Company, or makes provision satisfactory to the Company for payment of, any
federal, state or local withholding taxes that are required by law to be withheld in respect of
this option, if any.

7. Transfer Restrictions.

     (a) This option may not be sold, assigned, transferred, pledged or otherwise encumbered by the
Participant, either voluntarily or by operation of law, except by will or the laws of descent and
distribution, and, during the lifetime of the Participant, this option shall be exercisable only by
the Participant.

     (b) The Participant agrees that he or she will not transfer any Common Stock issued pursuant
to the exercise of this option unless the transferee, as a condition to such transfer, delivers to
the Company a written instrument confirming that such transferee shall be bound by all of the terms
and conditions of Section 4 and Section 5; provided that such a written confirmation shall not be
required with respect to (1) Section 4 after such provision has terminated in accordance with
Section 4(g) or (2) Section 5 after the completion of the lock-up period in connection with the
Company’s initial underwritten public offering.

8. Section 409A.

     This option is intended to comply with the provisions of Section 409A and shall be construed
and interpreted consistently therewith. Notwithstanding the foregoing, the Company shall have no
liability to the Participant or to any other person in the event that the option is determined to
not be compliant with Section 409A.

9. Provisions of the Plan.

     This option is subject to the provisions of the Plan (including the provisions relating to
amendments to the Plan and the provisions relating to governing law), a copy of which is furnished
to the Participant with this option.

-5-

 

     IN WITNESS WHEREOF

 KIOR, Inc.

	 	 	 	 	 	 	 

	 

	 	Name:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	Title:	 	 	 	 
	 

	 	 	 	 

	 	 

     PARTICIPANT’S ACCEPTANCE

     The undersigned hereby accepts the foregoing option and agrees to the terms and conditions
thereof. The undersigned hereby acknowledges receipt of a copy of the Company’s Amended and
Restated 2007 Stock Option/ Stock Issuance Plan.

	 	 	 	 	 	 	 

	 

	 	PARTICIPANT:	 	 
	 
	 	 	 	 	 	 
	 	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	Address:	 	 	 	 
	 

	 	 	 	 

	 	 
	 

	 	 	 	 

	 	 

-6-

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