In the case of discounts on “bundles” of products and/or services which include EnergyProducts, Codexis may with notice to MUS calculate the Net Sales by discounting the bonafide list price of an Energy Product by no more than the average percentage discount of allproducts and services of Codexis and/or its Affiliates in a particular “bundle”, calculatedas follows:         Average percentage      discount on a = (1 — A/B) x 100  particular “bundle"    where A equals the total discounted price of a particular “bundle” of products and services,and B equals the sum of the undiscounted bona fide list prices of each unit of every productand service in such “bundle”. Codexis shall provide MUS documentation, reasonablyacceptable to MUS, establishing such average discount with respect to each “bundle”. IfCodexis cannot so establish the average discount of a bundle, the Net Sales shall be basedon the undiscounted list price of the Energy Product in the bundle. If an Energy Product ina bundle is not sold separately and no bona fide list price exists for such Energy Product,the Parties shall negotiate in good faith an imputed list price for such Energy Product, andNet Sales with respect thereto shall be based on such imputed list price.2. The following definitions in Article 1 shall be amended to read as follows:     1.55 **“Reserved SubField Termination Date”**shall mean (a) for SubFields 1, 2, 4, 5, 6and 7, the period commencing on the Amendment Date and ending on the later of (i) five (5)years after Amendment Date, or (ii) a Separation Event, and (b) for SubFields 3, 8, 9 and 10(the “Modified SubFields”), the period commencing on the Amendment Date and ending six (6)years after the Amendment Date; provided, however, that in the event Codexis has satisfiedthe criteria set forth in Section 2.1.6(a) as to a particular SubField within the ModifiedSubFields such that such entire SubField becomes included in the Codexis Field, as providedin Section 2.1.6(d), on or before six (6) years after the Amendment Date, then the ReservedSubField Termination Date shall be extended by one additional year; and further providedthat upon the satisfaction of the criteria set forth in Section 2.1.6(d) for each additionalSubField within the Modified SubFields, if any, the Reserved SubField Termination Date forthe remaining Modified SubFields shall be extended for an additional one (1) year period, upto a maximum of three (3) such additional one (1) year extensions.     1.56 **“Reserved SubFields”**shall mean, in the period from the Amendment Date until theapplicable Reserved SubField Termination Date, the subject matter within the applicableSubField(s). It is understood and agreed that as of the applicable Reserved SubFieldTermination Date, (a) one or more Categories within the Reserved SubFields may become partof the Codexis Field pursuant to Section 2.1.6(c), (b), one or more of the ReservedSubFields may become part of the Codexis Field pursuant to Section 2.1.6(d), and (c) anyCategory and any Reserved SubField that is not within the scope of the Codexis Fieldpursuant to subsection (a) or (b) above as of the applicable Reserved
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SubField Termination Date, shall be terminated, and shall no longer be within theReserved SubFields.     1.57 **“Scheduled Product”**shall mean any Product described on Exhibit F.     1.59 **“Supplemental Product”**shall mean any Biocatlyst or Enzyme Product, and/orchemical made with the use of a Biocatlyst or Enzyme Product, in each case, that is (a)within a Category, where Codexis conducts with regard to such Category a research projectmeeting the criteria set forth in Section 2.1.6(a) prior to the applicable Reserved SubFieldTermination Date, and (b) within a Reserved SubField that becomes part of the Codexis Fieldat any time prior to the applicable Reserved SubField Termination Date pursuant to Section2.1.6(d).”3. Section 2.1.1 is amended as follows:a. In the first clause, revise the phrase “. . . worldwide, royalty-free (subject to Section2.1.5(b) licenses, . . .” to read: “. . . worldwide, royalty-free (subject to Section2.1.5(b) and the terms of Article 5) licenses, . . .”b. Revise Sections 2.1.1(a)(i), 2.1.1(a)(ii), 2.1.1(d)(i) and 2.1.1(d)(ii) by adding thephrase “and/or Section 2.1.6(d)” after each occurrence of the phrase “pursuant to Section2.1.6(c)”.c. Revise Section 2.1.1 by changing each occurrence of “the Reserved SubField TerminationDate” to “the applicable Reserved SubField Termination Date”.4. Section 2.1.6 is amended as follows:Revise Section 2.1.6 by changing each occurrence of “the Reserved SubField Termination Date”to “the applicable Reserved SubField Termination Date”.5. Section 2.1.6(h) is amended in its entirely as follows:“Except with respect to (i) any Category for which Codexis has satisfied the criteria setforth in Section 2.1.6(c), and (ii) any Reserved SubField for which Codexis has satisfiedthe criteria set forth in Section 2.1.6(d), it is understood and agreed that as of theapplicable Reserved SubField Termination Date, the applicable Reserved SubFields (includingeach Category and SubField) shall be terminated and shall have no content or force or effectfor the remainder of the term of the Agreement, and, as of the applicable Reserved SubFieldTermination Date, MUS (and/or its designee) shall have, as between the Parties, theexclusive rights in and to and shall be free, at its sole discretion, to work in, suchReserved SubField(s) without restriction or obligation to Codexis.”6. Article 5 shall be revised to read in its entirety as follows:
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     5.1 Codexis Stock. In partial consideration for the rights granted hereunder,Codexis shall issue to MUS one million (1,000,000) shares of Common Stock and six million(6,000,000) shares of Series A Preferred Stock of Codexis pursuant to the Stock Issuance andAsset Contribution Agreement by and between MUS and Codexis of even date hereof.     5.2 Energy Products. In consideration for the rights granted to Codexis inthis Amendment No. 3, for all Energy Products and/or any grant of rights with regard to theuse of any Enabling Technology for the development and commercialization of any EnergyProduct, Codexis will pay MUS:          5.2.1 [****] of all consideration received by Codexis from any Sublicensee or ThirdParty for:               a. option and/or license fees for rights to use any Enabling Technology to developand/or make any Energy Product; and               b. development payments (e.g., milestone payments) in respect of any Energy Product,and/or any product made with the use of any Energy Product; and               c. royalties and/or other payments for the commercialization of any Energy Product,and/or any product made with the use of any such Energy Product; and               d. the purchase of any equity securities of Codexis; provided, that the considerationreceived by Codexis from such Sublicensee or Third Party in connection with such purchaseshall be deemed to be the amount obtained by multiplying **[****]**; provided that at the timeof such purchase such Sublicensee or Third Party has a contractual relationship with Codexis(or proposes to have a contractual relationship with Codexis in connection with suchpurchase and the contractual relationship thereafter becomes effective), and the primarybusiness purpose of the relationship is the development and/or commercialization of (i) anyEnergy Product, or (ii) any product made with the use of any Energy Product; and          5.2.2 Notwithstanding anything to the contrary in Section 5.2.1 above, Codexis shallnot be required to pay to MUS any share of research and/or development funding received (andnot subject to any further performance criteria) by Codexis from a Third Party for thesupport of Codexis personnel (i.e., payments on an FTE basis to support Codexis employeesfor activities conducted by Codexis); provided that (i) such payments are actually used byCodexis for FTE funding, and (ii) the applicable rate per * Certain information on this page has been omitted and filedseparately with the Securities and Exchange Commission. Confidential treatmenthas been requested with respect to the omitted portions.
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FTE does not exceed the Base FTE Rate. The Base FTE Rate for 2006 shall be **[****]**perFTE per year, and shall be revised annually at the beginning of each subsequent calendaryear to reflect annual changes in the Consumer Price Index, using September 2006 as thebaseline comparison. Codexis shall pay to MUS **[****]**of any research funding received from aThird Party for the development of any Energy Product, and/or any product made with the useof any Energy Product, in each case only to the extent such funding does not satisfy thecriteria listed in subsections (i) and (ii) above.          5.2.3 If Codexis directly commercializes any Energy Product, Codexis will pay to MUS aroyalty of **[****]**of (a) Net Sales of such Energy Products sold by Codexis or itsAffiliates, and/or (b) amounts received by Codexis or its Affiliates from any Sublicensee orother Third Party for the use of Energy Products, to the extent Codexis or its Affiliatesutilize such Product(s) to provide services to such Sublicensee or Third Party, as the casemay be.     5.3 Quarterly Reports. Commencing in the first calendar quarter in whichCodexis receives any payment subject to Section 5.2, Codexis shall make quarterly writtenreports to MUS within sixty (60) days after the end of each calendar quarter, stating ineach such report the consideration subject to Section 5.2 received by it during suchcalendar quarter. Such reports shall provide separately for Codexis and each of itsAffiliates and Sublicensees, in each case, on a country-by-country and EnergyProduct-by-Energy Product basis: (i) the type (e.g., license fee, milestone payment)and amount of consideration received;  (ii) for payments based on Energy Products, thequantity and description of each such Energy Product sold or used; and  (iii) the calculation of amounts due to MUS,accompanied by sufficient information to enable MUS to verify theaccuracy of the calculations made by Codexis, and a detailedexplanation of the methodology used to determine the applicablepayment.     5.4 Payment. Concurrently with providing to MUS each quarterly reportdescribed in Section 5.3, Codexis shall pay MUS all amounts due under Section 5.2 for thecalendar quarter corresponding to such report.     5.5 Audit. Codexis and its Affiliates shall keep complete, true and accuratebooks of account and records for the purpose of determining the amounts payable underSection 5.2 of this Agreement. Such books and records shall be kept at the principal placeof business of such party, as the case may be, for at least four (4) years following the endof the calendar quarter to which they pertain. Such records will be open for inspectionduring such four (4) year period by a public accounting firm selected by MUS reasonablyacceptable to Codexis, solely for the purpose of verifying the reports and * Certain information on this page has been omitted and filedseparately with the Securities and Exchange Commission. Confidential treatmenthas been requested with respect to the omitted portions.
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payments hereunder. Such inspections may be made no more than once each calendar year,at reasonable times and on reasonable notice. Inspections conducted under this Section 5.5shall be at the expense of MUS, unless a variation or error producing an increase exceedingten percent (10%) of the amount stated for any period covered by the inspection isestablished in the course of any such inspection, whereupon all reasonable costs relating tothe inspection and any unpaid amounts that are discovered will be paid promptly by Codexistogether with interest thereon as set forth in Section 5.6 below.     5.6 Payment Method; Late Payments. All payments due to MUS under thisAgreement shall be paid in U.S. dollars by bank wire transfer in immediately available fundsto a bank account designated by MUS. Any payment or portion thereof that is not paid on thedate such payments are due under this Agreement shall bear interest at the lesser of (i) theprime rate as reported by the Chase Manhattan Bank, New York, New York (or its successor) onthe date such payment is due, plus an additional two percent (2%), or (ii) the maximum ratepermitted by law, in each case calculated on the number of days such payment is delinquent.This Section 5.6 shall in no way limit any other remedies available for late payment.     5.7 Currency Conversion. All payments due to MUS under this Agreement shallfirst be determined in local currency and then, if necessary, converted to its equivalent inUnited States currency. The buying rates of exchange for converting the currencies involvedinto the currency of the United States quoted by the Wall Street Journal (or itssuccessor in interest) on the last business day of the quarterly period in which thepayments were received by Codexis shall be used to determine any such conversion.     5.8 Restrictions on Payment. The obligation of Codexis to pay amounts to MUSunder this Agreement with respect to sales of Energy Products in a particular country shallbe waived and excused to the extent that statutes, laws, codes or government regulations ina particular country prevent such payments; provided, however, in such event, if legallypermissible, Codexis shall pay the amounts owed to MUS by depositing such amounts in a bankaccount in such country that has been designated by MUS and promptly report such payment toMUS in writing.     5.9 Taxes. Any tax that Codexis is required to withhold and pay on behalf ofMUS with respect to amounts payable to MUS under this Agreement shall be deducted from andoffset against said payments prior to remittance to MUS; provided, however, that in regardto any tax so deducted, Codexis shall give or cause to be given to MUS such assistance asmay reasonably be necessary to enable MUS to claim exemption therefrom or credit therefor,and in each case shall furnish MUS with proper evidence of the taxes paid on its behalf.     5.10 Energy Affiliate.          (a) If (i) Codexis or any of its Affiliates or subsidiaries (each, a **“Codexis Entity"**)proposes to form, establish or acquire, directly or indirectly, any Affiliate or subsidiarythat engages in a line of business related to the use of any Energy
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Products, and/or any Enabling Technology in or for any energy application (the **“EnergyRights"**), or any Affiliate or subsidiary of Codexis proposes, at any time, to engage,directly or indirectly, in such line of business (in each case, an **“Energy Affiliate"**); (ii)a Codexis Entity proposes to acquire or obtain, directly or indirectly, by merger,consolidation, acquisition of equity interests or otherwise, any assets, rights or otherinterests of whatever kind and nature in any business or Third Party (e.g. any individual,corporation, partnership, limited liability company, joint venture or other businessorganization or division thereof) that engages in a line of business related to the use ofany of the Energy Rights (or at any time in the future proposes to engage in such line ofbusiness); or (iii) a Codexis Entity proposes to acquire or obtain, directly or indirectly,by merger, consolidation, acquisition of equity interests or otherwise, or becomes entitledto, any assets, rights or other interests of whatever kind and nature in any business orThird Party, in whole or partial consideration for the sale, assignment, license,contribution, pledge or other transfer by a Codexis Entity of any assets, interests orrights relating to any of the Energy Rights, then Codexis shall give written notice to MUSat least thirty (30) days prior to the effectiveness or consummation of such event ortransaction. The notice shall describe in reasonable detail the proposed event ortransaction including, without limitation, the nature of such event or transaction, theconsideration to be paid and the amount constituting the applicable MUS Interest (as definedin Section 5.10(b) below).          (b) In consideration for the rights granted to Codexis in this Amendment No. 3, Codexisshall take, or cause to be taken, all actions, and do, or cause to be done, all thingsnecessary, proper and advisable under applicable laws, so as to assign, transfer and deliverthe MUS Interest to MUS immediately upon the effectiveness or consummation of any event ortransaction described in Section 5.10(a) above or cause the MUS Interest to be so assigned,transferred and delivered, without cost to MUS. For purposes of this Section 5.10, the term**“MUS Interest”**shall mean all legal and beneficial title to the equity interests, assets,rights or other interests of whatever kind and nature (other than consideration received byCodexis subject to Codexis’ payment obligations to MUS pursuant to Section 5.2.1 above) ofthe Energy Affiliate or Third Party in an amount equal to **[****]**of each asset, interest orright held, acquired or obtained by the Codexis Entity(ies) in connection with any event,transaction or series of transactions described in Section 5.10(a) above.          (c) If, in connection with the transaction or series of transactions described inSection 5.10(a), a Codexis Entity has provided consideration other than assets, interests orrights relating to the use of any of the Energy Rights (the “**Other Consideration**”), then, asa condition of the transfer to MUS of the portion of the MUS Interest held, acquired orobtained by the Codexis Entity specifically for such Other Consideration, MUS shallreimburse the Codexis Entity for up to **[****]**of the cash value of the Other Consideration(as of the date of transfer of the Other Consideration by the Codexis Entity). The electionto reimburse the Codexis Entity and the amount of such * Certain information on this page has been omitted and filedseparately with the Securities and Exchange Commission. Confidential treatmenthas been requested with respect to the omitted portions.
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reimbursement (up to the aforementioned **[****]**limit) shall be determined by MUS in itssole discretion. Upon reimbursement, the Codexis Entity shall transfer to MUS theapplicable portion of the MUS Interest attributable to the amount reimbursed by MUS for theOther Consideration. If MUS elects to reimburse the Codexis Entity for a portion of theOther Consideration corresponding to the MUS Interest equal to less than **[****]**of suchOther Consideration, and not for the total **[****]**, MUS’ right to receive additional equityinterests, assets, rights or other interests of whatever kind and nature of the applicableEnergy Affiliate or Third Party pursuant to Section 5.10(b) that are directly attributableto the equity interests, assets, rights or other interests held, acquired or obtained forsuch Other Consideration will be prorated accordingly. For example, if MUS elects toreimburse the Codexis Entity for **[****]**of the Other Consideration corresponding to the MUSInterest (and not **[****]**), MUS’ right to receive additional equity interests, assets, rightsor other interests of whatever kind and nature of the applicable Energy Affiliate or ThirdParty pursuant to Section 5.10(b) that are directly attributable to the equity interests,assets, rights or other interests held, acquired or obtained for such Other Considerationwill be equal to **[****]**of the amount that MUS would have received if MUS had reimbursed theCodexis Entity for **[****]**of the Other Consideration corresponding to the MUS Interest. IfMUS elects not to pay any amount to the Codexis Entity for the reimbursement of the OtherConsideration, MUS’ right to receive additional equity interests, assets, rights or otherinterests of whatever kind and nature of the applicable Energy Affiliate or Third Partypursuant to Section 5.10(b) that are directly attributable to the equity interests, assets,rights or other interests held, acquired or obtained for such Other Consideration shallterminate. Except as otherwise provided in this Section 5.10(c) with respect to an electionby MUS to reimburse the applicable Codexis Entity for Other Consideration, MUS shall, in allcases, be entitled to receive, and shall not be required to reimburse any Codexis Entity,Energy Affiliate or Third Party or otherwise pay any amounts to any Codexis Entity, EnergyAffiliate or Third Party for, the MUS Interest and any additional equity interests, assets,rights or other interests of the applicable Energy Affiliate or Third Party that areattributable to or received in consideration for any of the Energy Rights (and notattributable to or received in consideration for Other Consideration).          (d) If any Codexis Entity proposes to subsequently sell, assign, or otherwise transferany assets, rights or interests acquired or obtained in connection with an event,transaction or series of transactions described in Section 5.10(a) above, then Codexis shallgive written notice to MUS at least thirty (30) days prior to the effectiveness orconsummation of such transaction, which notice shall describe the proposed transaction inreasonable detail, including, without limitation, the nature of such transaction and theconsideration to be received. MUS shall have the right, exercisable upon written notice toCodexis within fifteen (15) days after receipt of such notice, to participate in suchtransaction and to sell, assign or otherwise transfer up to a pro rata portion of the MUSInterest on the same terms and conditions as described in the notice; provided, however,that in no event shall MUS be required to sell, assign or transfer any * Certain information on this page has been omitted and filedseparately with the Securities and Exchange Commission. Confidential treatmenthas been requested with respect to the omitted portions.
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portion of the MUS Interest to any party, except as required by applicable law;provided, further, that MUS’ pro rata portion of the MUS Interest shall be deemed to be**[****]**of each asset, right or interest proposed to be sold, assigned or transferred by theapplicable Codexis Entity(ies).          (e) Notwithstanding the foregoing, if for any reason all or any portion of the MUSInterest is not transferable to MUS in accordance with Section 5.10(b) above, or if thesale, assignment or other transfer by MUS of all or any portion of the MUS Interest inaccordance with Section 5.10(d) above is not permitted, then the applicable CodexisEntity(ies) shall not consummate or effectuate, directly or indirectly, such event ortransaction without the prior written consent of MUS in its sole discretion.          (f) In the event that (i) sufficient information does not exist to determine the value,amount or allocation of any assets, rights or interests for purposes of calculating theapplicable MUS Interest, the applicable Other Consideration or any other amount inaccordance with this Section 5.10, or (ii) Codexis and MUS cannot otherwise agree as to suchvalue, amount or allocation, such value, amount or allocation shall be determined through anappraisal to be performed by an independent Third Party reasonably acceptable to bothParties, and the expenses incurred in obtaining such appraisal shall be shared equally byCodexis and MUS.          (g) In furtherance of the foregoing, Codexis acknowledges that, in consideration forthe rights granted to Codexis in this Amendment No. 3, this Section 5.10 is intended toprovide MUS with the applicable portion of any value or potential value attributable to orderived from any business related to energy applications engaged in by any Codexis Entity orotherwise attributable to or derived from any of the Energy Rights and agrees that it shallnot authorize, commit or agree to take, and shall not permit any Affiliate, nor anysubsidiary, to authorize, commit or agree to take, any action that would be inconsistentwith this Section 5.10 or impair any portion of the MUS Interest.     5.11 MUS not an Affiliate. Notwithstanding anything to the contrary, for purposes ofthis Article 5, MUS shall not be considered, or deemed to be, an Affiliate of Codexis.7. Article 12 of the Agreement is amended by the addition of new Section 12.7:     12.7 Termination for Cause. In the event that Codexis materially breaches anyof its obligations pursuant to Article 5 of the Agreement, and such breach has continued forsixty (60) days after receipt of written notice thereof from MUS, MUS may terminate any andall rights received by Codexis under the terms of this Amendment No. 3.8. Exhibit F shall be revised such that Exhibit F shall read in its entirety as attached to thisAmendment No. 3. * Certain information on this page has been omitted and filedseparately with the Securities and Exchange Commission. Confidential treatmenthas been requested with respect to the omitted portions.
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9. Exhibit G shall be revised such that Exhibit G shall read in its entirety as attached to thisAmendment No. 3.10. Except as expressly provided herein, the terms of the Agreement shall remain in full forceand effect.[THE REMAINDER OF THIS PAGE HAS BEEN INTENTIONALLY LEFT BLANK]
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     IN WITNESS WHEREOF, MUS and Codexis have executed this Amendment No. 3 to License Agreement asof the first above written.       MAXYGEN, INC. CODEXIS, INC.       By: /s/ Russell J. Howard By: /s/ Alan Shaw       Name: Russell J. Howard Name: Alan ShawTitle: Chief Executive Officer Title: President
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**Exhibit F**