Document:

Description of 2006 Executive Officer Cash Bonus Plan

 Exhibit 10.1 
 DESCRIPTION OF EXECUTIVE OFFICER CASH BONUS PLAN 
 Maxygen, Inc. (the “Company”) maintains a Cash Bonus Plan for executive officers and certain other officers of the Company that is designed to
reward participants based on their individual performance and the Company’s financial and other performance. 
 Under the Cash Bonus
Plan, annual bonus amounts are determined based on specified weighting of factors relating to executive officer’s individual performance, the overall financial performance of the Company and other performance targets. The annual financial and
other targets for the Cash Bonus Plan are set by the Compensation Committee of the Company’s Board of Directors and are currently based on the company’s financial performance (revenue and cash burn), product development goals and other
objectives. 
 The Company’s Chief Executive Officer is eligible to receive an annual cash performance bonus of between 0 and 100% of
base salary and the target bonus amount for the Company’s Chief Executive Officer is 40% of base salary. The Company’s executive officers (other than the Chief Executive Officer) are eligible to receive an annual cash performance bonus of
between 0 and 50% of base salary and the target bonus amount for these executive officers is 25% of base salary. Bonus payments are paid in one annual payment shortly after the end of each calendar year.Form of Amendment to Stock Option Agreements

 Exhibit 10.2 
 MAXYGEN, INC. 
 AMENDMENT TO STOCK
OPTION AGREEMENTS 
 This AMENDMENT TO STOCK
OPTION AGREEMENTS (the “Amendment”), dated                     , 2006, is made by
and between MAXYGEN, INC., a Delaware corporation (the “Company”), and                     
(the “Executive”). 
 WHEREAS, the Company and the Executive have entered into certain Stock
Option Agreements listed on Exhibit A hereto (collectively, the “Stock Option Agreements”); and 
 WHEREAS, the Compensation Committee of the Board of Directors of the Company believes that it is in the best interests of the Company’s stockholders to amend the Stock Option Agreements as provided
below. 
 NOW, THEREFORE, in consideration of the premises and the mutual covenants
herein contained, the Company and the Executive agree as follows: 
 1. Section 5.2 of each Stock Option Agreement is hereby amended to provide in
its entirety as follows: 
 “5.2 In the event of termination of Optionee’s continuous status as an employee,
director or consultant following a Change of Control of the Company, the post-termination exercise period of Executive’s outstanding stock option award shall extend to the later of the fifteenth day of the third month following the date at
which, or December 31 of the calendar year in which the stock option would otherwise have expired but for this extension, based on the terms of the stock option on its grant date; provided, however, that in the event final Treasury Regulations
under Code Section 409A permit a longer extension without resulting in the imposition of an additional tax under Code Section 409A, the stock option shall provide for such greater post-termination exercise period; provided, further, that
in no event shall the term of the stock option be extended longer than its original maximum term.” 
 2. Section 5.4 is amended by deleting
the existing subsection (iv) and inserting new subsection(s) (iv) and (v) as follows: 
 “or
(iv) payment by net exercise, or (v) payment by a combination of the methods of payment permitted by subparagraph 5.4(i) through 5.4(iv) above.” 
 3. For purposes of this Agreement, Change of Control shall have the meaning set forth in that certain Change of Control Agreement entered by the Company and the Executive dated March 3, 2003, as subsequently amended,
including, without limitation, any amendment thereto after the date of this Amendment.  

 4. Except as expressly provided herein, the terms of each Stock Option Agreement shall remain in full force and
effect. 
  

			
	MAXYGEN, INC.
		
	By:	 	  

		 	Louis Lange, Chairman of Maxygen
		 	Compensation Committee
	
	THE EXECUTIVE
	
	  

  

 2 

 Exhibit A 
 Stock Option Agreements 
 Grant Date 
  

 3Form of Amendment No. 2 to Change of Control Agreement

 Exhibit 10.3 
 MAXYGEN, INC. 
 AMENDMENT NO. 2 TO 

CHANGE OF CONTROL AGREEMENT 
 This AMENDMENT NO. 2 TO CHANGE OF CONTROL
AGREEMENT (the “Amendment No. 2”), dated                     , 2006, is made by and between
MAXYGEN, INC., a Delaware corporation (the “Company”), and                      (the
“Executive”). 
 WHEREAS, the Company and the Executive have entered into a Change of Control
Agreement dated June 29, 2001 (the “Original Agreement”); and 
 WHEREAS, the Company and
the Executive have entered into an Amendment No. 1 to Change of Control Agreement dated March 3, 2003 (“Amendment No. 1”); and 
 WHEREAS, the Compensation Committee of the Board of Directors of the Company believes that it is in the best interests of the Company’s stockholders to amend the Original
Agreement and Amendment No. 1 as provided below. 
 NOW, THEREFORE, in consideration
of the premises and the mutual covenants herein contained, the Company and the Executive agree as follows: 
 1. The
definitions shall be amended as follows: 
 1.1 Section 2(f), the definition of “Change of Control,” is hereby amended
as follows: 
  

	 	1.1.1	Clause (iii) of the definition of “Change of Control” is hereby amended and restated in its entirety as follows: 

 “(iii) a merger, recapitalization, reorganization, consolidation or other similar transaction (a “Business Combination”) in which
beneficial ownership of securities of the Company representing at least thirty-five percent (35%) of the combined voting power entitled to vote in the election of directors has changed.” 
  

	 	1.1.2	Clauses (iv) and (v) of the definition of “Change of Control” are hereby amended by replacing the phrase “fifty percent (50%)” in each such
clause with the phrase “thirty-five percent (35%).” 

  

	 	1.1.3	New clause (viii) is added to the end of the definition of “Change of Control” as follows: 

 “or (viii) the consummation by the Company of a Business Combination with respect to which all or substantially all of the individuals and
entities who were the beneficial owners of the combined voting power of the then outstanding securities of the Company entitled to vote generally in the election of directors immediately prior to such Business Combination do not, following
consummation of all transactions intended to constitute part of such Business Combination, beneficially own, directly or indirectly, at least sixty-five percent (65%) of the voting securities of the Company (or the corporation, business trust
or other entity resulting from or being the surviving entity in such Business Combination).” 

 2. The benefits in the event of a Change of Control shall be amended as follows:

 2.1 Clause (ii) of the first sentence of Section 3(a) following the colon is amended in its entirety to also provide for
the full accelerated vesting of restricted stock units and performance shares as follows: 
 “(ii) each of the Executive’s
outstanding stock options, all stock subject to repurchase or forfeiture, including without limitation, restricted stock, restricted stock units and performance shares awards, and any options, stock subject to repurchase or forfeiture, awards or
purchases held in the name of an estate planning vehicle for the benefit of the Executive or his or her immediate family, shall have their vesting and exercisability schedule accelerate in full (or, as applicable, the corresponding repurchase or
forfeiture right shall lapse in full) as of the date of termination.” 
 2.2 Clause (i) of the first sentence of
Section 3(b) is amended in its entirety to also provide for the pro-rata accelerated vesting of restricted stock units and performance shares as follows: 
 “(i) each of the Executive’s outstanding stock options, all stock subject to repurchase or forfeiture, including without limitation restricted stock, restricted stock units, performance shares awards, and
any options, stock subject to repurchase or forfeiture, awards or purchases held in the name of an estate planning vehicle for the benefit of the Executive or his or her immediate family, shall have their vesting and exercisability schedule
accelerated such that vesting (or, as applicable, the corresponding repurchase or forfeiture right lapsing) shall occur as if the vesting (or lapsing) had occurred on a monthly basis from the last date of vesting (or lapse) to the date of
termination.” 
 2.3 New clause (iv) is added to the end of the first sentence of Section 3(a) to provide for the
extension of the post-termination exercise period of any outstanding stock option or stock appreciation right as follows: 
 “and
(iv) the post-termination exercise period of Executive’s outstanding stock option and stock appreciation right awards shall automatically be extended to the later of (A) the fifteenth day of the third month following the date at which
the stock option or stock appreciation right would otherwise have expired but for this extension, based on the terms of the stock option or stock appreciation right on its grant date, or (B) December 31 of the calendar year in which the
stock option or stock appreciation right would otherwise have expired but for this extension, based on the terms of the stock option or stock appreciation right on its grant date; provided, however, that in the event final Treasury Regulations under
Code Section 409A permit a longer extension without resulting in the imposition of an additional tax under Code Section 409A, the stock option or stock appreciation right shall provide for such greater post-termination exercise period;
provided, further, that in no event shall the term of the stock option or stock appreciation right be extended longer than its original maximum term.” 

 2.4 New Section 3(g) is hereby added as follows: 
 “(g) Code Section 409A. Notwithstanding any contrary provision of the Agreement, if the Company determines, in its good faith judgment,
that Section 409A of the Code shall result in the imposition of additional tax on any payment or benefit otherwise due to the Executive under the Agreement during the six (6) month period following the Executive’s termination date,
all such payments or benefits shall accrue during the six (6) month period and shall become payable in a lump sum payment on the date six (6) months and one (1) day following the Executive’s termination date. All subsequent
payments or benefits, if any, shall be paid as provided in the Agreement. 
 3. Except as expressly provided herein, the terms of the Original
Agreement and Amendment No. 1 shall remain in full force and effect. 
  

			
	MAXYGEN, INC.
		
	By:	 	  

		 	Louis G. Lange, Chairman of Maxygen
		 	Compensation Committee
	
	THE EXECUTIVE

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