Document:

EX-10.4.1

Exhibit 10.4.1

AMENDMENT TO EMPLOYMENT AGREEMENT

     This amendment (this “Amendment”) is entered into as of this 31st day of December, 2008, by
and between Atlas Air, Inc., a Delaware corporation (“Atlas”), and William J. Flynn (the
“Employee”).

     WHEREAS, the parties hereto previously entered into an employment agreement dated as of April
21, 2006 (the “Employment Agreement”); and

     WHEREAS, in order to, among other things, comply with Section 409A of the Internal Revenue
Code of 1986, as amended (“Section 409A”), the parties hereto wish to amend the Employment
Agreement in accordance with the terms set forth herein;

     NOW, THEREFORE, in consideration of the mutual covenants and agreements set forth herein and
other good and valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties hereto agree as follows:

     1. A new sentence is added to the end of Section 1.3 of the Employment
Agreement to read as follows:

“Notwithstanding the foregoing, in the event that, as a result of an absence
because of mental or physical incapacity or other impairment, the Employee incurs
an earlier “separation from service” within the meaning of Section 409A, the
Employee shall on such date automatically be terminated from employment with
Atlas, and the Employment Period will terminate, as a result of Permanent
Disability.”

     2.
Section 1.4 of the Employment Agreement is amended in its entirety to
read as follows:

     “1.4 “Change of Control” means the acquisition by any person, entity,
or “group” (within the meaning of Final Treasury Regulation §
1.409A-3(i)(5)(v)(B), excluding for this purpose any employee benefit plan of
Atlas or its affiliates) of beneficial ownership (applying the attribution rules
set forth in Final Treasury Regulation § 1.409 A-3(i)(5)(iii)) of greater than
fifty percent (50%) of the total voting power of the outstanding voting securities
of either Atlas or of Atlas Air Worldwide Holdings, Inc. (“Holdings”) entitled to
vote generally in the election of directors.”

 

 

     3. The penultimate sentence of Section 3.2 of the Employment Agreement is
amended in its entirety to read as follows:

“Any bonus paid under the Annual Incentive Plan will be paid no later than two
weeks following the completion of the year-end audit for the applicable year, but
in no event later than March 15 of the year following the applicable year.”

     4. Section 4.2(a) of the Employment Agreement is amended in its entirety to
read as follows:

     “(a) If the Employment Period is terminated by Atlas for reasons other than
Cause or if the Employment Period is terminated by the Employee for Good Reason,
and subject to the Employee’s execution of a release upon terms and conditions
consistent with this Agreement and acceptable to Atlas and Employee, which release
must be presented to Employee upon or promptly after termination of the Employment
Period, fully executed and become effective before the six-month anniversary of the
date on which the Employment Period terminates, then the Employee shall be entitled
to receive:

	 	(i)	 	an amount equal to one and one-half times the
Employee’s then-current Annual Base Salary, with one-third of such
amount payable in a lump-sum on the first day of the seventh month
following the date on which the Employment Period terminates (the
“Lump-Sum Payment Date”), and with the remaining two-thirds of such
amount payable in accordance with Atlas’ normal pay schedule
beginning on the day after the Lump-Sum Payment Date and continuing
through the first anniversary of the Lump-Sum Payment Date; and
	 
	 	(ii)	 	continued coverage for a period of twelve months
immediately following the date on which the Employment Period
terminates under the health (medical, dental, and vision) and life
insurance programs of Atlas (or, if continued coverage under such
Atlas programs is not available or practicable, then receive coverage
under substantially similar individual health and life insurance
policies for such twelve-month period); provided that such coverage
will cease immediately in the event the Employee

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	 	 	 	obtains comparable coverage in connection with subsequent
employment.

The above benefits are in addition to the Employee’s right to receive accrued but
unused vacation pay through the employment termination date, and all other
benefits in which the Employee is vested pursuant to other plans and programs of
Atlas at the time of the employment termination date.”

     5. Section 4.2(b) of the Employment Agreement is amended in its entirety to
read as follows:

     “(b) Upon the death or Permanent Disability of the Employee during the
Employment Period, the Employment Period shall terminate and the Employee’s Base
Annual Salary that is accrued for the then-current pay period but unpaid as of the
date of such death or Permanent Disability shall be paid to the Employee or the
Employee’s personal representative, as applicable. In addition, upon the Permanent
Disability of the Employee, the Employee shall be entitled to the compensation and
benefit coverage set forth in Section 4.2(a) above. Further, upon the death of the
Employee, the Employee’s spouse shall be entitled to the compensation set forth in
Section 4.2(a) above, and the Employee’s spouse and covered dependents shall be
entitled to the benefit coverage set forth in Section 4.2(a) above, except that
that the payments under Section 4.2(a)(i) shall instead be made in a lump sum
within ten (10) days immediately following the Employee’s date of death.”

     6. Section 4.2(d) of the Employment Agreement is amended in its entirety to
read as follows:

     “(d) (i) If, within the twelve-month period immediately following a Change of
Control, the Employment Period is terminated by Atlas for reasons other than Cause
or if the Employment Period is terminated by the Employee for Good Reason, and
subject to the Employee’s execution of a release upon terms and conditions
consistent with this Agreement and acceptable to Atlas and Employee, which release
must be presented to Employee upon or promptly after termination of the Employment
Period, fully executed and become effective before the six-month anniversary of
the date on which the Employment Period terminates, then the Employee shall be
entitled to (and not in addition to) the compensation and benefit coverage set
forth in Section 4.2(a) above, except that the amount of the payments under
Section 4.2(a)(i) above shall

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be equal to two times the Employee’s then-current Annual Base Salary, with
one-fourth of such amount payable in a lump sum on the Lump-Sum Payment Date, and
with the remaining three-fourths of such amount payable in accordance with Atlas’
normal pay schedule beginning on the day after the Lump-Sum Payment Date and
continuing through the 18-month anniversary of the Lump-Sum Payment Date.

     (ii) If, within the six-month period immediately following a termination of the
Employment Period by Atlas for reasons other than Cause or by the Employee for Good
Reason, a Change of Control occurs, then, in addition to the payments set forth in
Section 4.2(a)(i) above, the Employee shall receive payments in an amount equal to
one-half of the Employee’s then-current Annual Base Salary, payable in accordance
with Atlas’ normal pay schedule beginning on the day after the first anniversary of
the Lump-Sum Payment Date and continuing for the six-month period immediately
thereafter.”

     7. The third sentence of Section 4.2(e)(iii) of the Employment Agreement is
deleted in its entirety.

     8. Section 4.2(e)(iv) of the Employment Agreement is amended in its
entirety to read as follows:

     “(iv) If a reduction is made pursuant to subparagraph (i), such reduction
will be made, first, to any post-employment payments being made to the Employee
under Sections 4.2(a), 4.2(b), or 4.2(d) above in accordance with Atlas’ normal
pay schedule, with such reduction being made in reverse order (i.e., the latest
payments are reduced first), and second, if further reductions are still required,
to any post-employment payment being made to the Employee under such Sections on
the Lump-Sum Payment Date, and third, if further reductions are still required, to
any post-employment benefit coverage being provided to the Employee under such
Sections.”

     9. A new Section 4.2(f) is added to the Employment Agreement to read as
follows:

     “(f) Notwithstanding any other provision of this Agreement to the contrary,
because the Employee is a “specified employee” (as that term is defined in Section
409A), to the extent that any payment or benefit under this Agreement constitutes
an amount payable or benefit to be provided under a “nonqualified deferred
compensation plan” (as defined in

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Section 409A) upon or as a result of a “separation from service” (as
defined in Section 409A) and which is not exempt from Section 409A, then,
notwithstanding any other provision in this Agreement to the contrary, such
payment or benefit provision will not be made to the Employee during the six-month
period immediately following his “separation from service” date. Instead, on the
first day of the seventh month following such “separation from service” date, all
amounts that otherwise would have been paid or provided to the Employee during
that six-month period, but were not because of this provision, will be paid or
provided to the Employee, with any cash payment delayed during such six-month
period to be made to the Employee in a single lump sum.”

     10. Continued Validity of the Employment Agreement. Except as amended
and superseded by this Amendment, the Employment Agreement will remain in full force
and effect, will continue to bind the parties hereto, and will continue to govern the terms
and conditions of the Employee’s continued employment with Atlas. To the extent that
the terms of this Amendment conflict or are inconsistent with the terms of the
Employment Agreement, the terms of this Amendment will govern.

     11. Amendment Effective Date. This Amendment will become binding and effective on December 31, 2008.

     12. Governing Law. This Amendment will be governed by and construed in
accordance with the laws of the State of New York, without reference to principles of
conflict of law.

     13. Counterparts. This Amendment may be executed in several counterparts,
each of which will be deemed to be an original, and all such counterparts when taken
together will constitute one and the same original.

[SIGNATURE PAGE FOLLOWS]

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IN WITNESS WHEREOF, the parties hereto have executed this Amendment to your Employment
Agreement dated April 21, 2006, on the day and year first written above, to be effective as of
December 31, 2008.

	 	 	 	 	 	 	 
	ATLAS AIR, INC.	 	WILLIAM J. FLYNN	 	 
	 
	 	 	 	 	 	 
	By:

	 	/s/ Adam R. Kokas
 

	 	/s/ William J. Flynn
 

	 	 
	Name: Adam R. Kokas	 	 	 	 
	Title:   Senior Vice President,	 	 	 	 
	 
	 	    General Counsel, Chief Human	 	 	 	 
	 
	 	    Resources Officer & Secretary	 	 	 	 

6EX-10.10.1

Exhibit 10.10.1

AMENDMENT TO EMPLOYMENT AGREEMENT

     This
amendment (this “Amendment”) is entered into as of this 31st day of December, 2008, by
and between Atlas Air, Inc., a Delaware corporation (“Atlas”), and John W. Dietrich (the
“Employee”).

     WHEREAS,
the parties hereto previously entered into an amended and restated employment
agreement dated as of September 8, 2006 (the “Employment Agreement”); and

     WHEREAS,
in order to, among other things, comply with Section 409A of the Internal Revenue
Code of 1986, as amended (“Section 409A”), the parties hereto wish to amend the Employment
Agreement in accordance with the terms set forth herein;

     NOW, THEREFORE, in consideration of the mutual covenants and agreements set forth herein and
other good and valuable consideration, the receipt and sufficiency of which are hereby
acknowledged, the parties hereto agree as follows:

     1. A new sentence is added to the end of Section 1.3 of the Employment
Agreement to read as follows:

“Notwithstanding the foregoing, in the event that, as a result of an absence
because of mental or physical incapacity or other impairment, the Employee incurs
an earlier “separation from service” within the meaning of Section 409A, the
Employee shall on such date automatically be terminated from employment with
Atlas, and the Employment Period will terminate, as a result of Permanent
Disability.”

     2. Section 1.4
of the Employment Agreement is amended in its entirety to read as follows:

     “1.4
“Change of Control” means the acquisition by any person,
entity, or “group” (within the meaning of Final Treasury Regulation §
1.409A-3(i)(5)(v)(B), excluding for this purpose any employee benefit plan of
Atlas or its affiliates) of beneficial ownership (applying the attribution rules
set forth in Final Treasury Regulation § 1.409A-3(i)(5)(iii)) of greater than
fifty percent (50%) of the total voting power of the outstanding voting securities
of either Atlas or of Atlas Air Worldwide Holdings, Inc. (“Holdings”) entitled to
vote generally in the election of directors.”

 

 

     3. The first sentence of Section 3.1 of the Employment Agreement is
amended in its entirety to read as follows:

     “Atlas will pay Employee a base annual salary (the “Base Annual Salary”) of USD $467,500.00
per annum, payable in semi-monthly installments.”

     4. The penultimate sentence of Section 3.2 of the Employment Agreement is
amended in its entirety to read as follows:

“Any bonus paid under the Annual Incentive Plan will be paid no later than two
weeks following the completion of the year-end audit for the applicable year, but
in no event later than March 15 of the year following the applicable year.”

     5. The second sentence of Section 3.4 of the Employment Agreement is
amended in its entirety to read as follows:

     “Atlas reserves the right to discontinue participation in any health insurance plan
at any time, provided that Atlas will reimburse the Employee for his cost of obtaining
comparable health care benefits for him and his dependents during the Employment Period,
which reimbursement will be made by Atlas no later than March 15 of the year following
the year in which the expense being reimbursed is incurred, provided that the Employee
timely submits any such reimbursement request to Atlas in accordance with procedures
established by Atlas from time to time.”

     6. Section 4.2(a) of the Employment Agreement is amended in its entirety to
read as follows:

     “(a) If the Employment Period is terminated by Atlas for reasons other than
Cause or if the Employment Period is terminated by the Employee for Good Reason,
and subject to the Employee’s execution of a general release upon terms and
conditions consistent with this Agreement and acceptable to Atlas and Employee,
which release must be presented to Employee upon or promptly after termination of
the Employment Period, fully executed and become effective before the six-month
anniversary of the date on which the Employment Period terminates, then the
Employee shall be entitled to receive:

	 	(i)	 	an amount equal to eighteen (18) months of the
Employee’s then-current monthly Base Salary, payable in a lump-sum on
the first day of the seventh month following the date on

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	 	 	 	which the Employment Period terminates (the “Lump-Sum Payment
Date”);

	 	(ii)	 	in accordance with Atlas’ Relocation Policy for
Executive Homeowners/Renters in effect as of January 1, 2009 (or any
subsequent Atlas Relocation Policy that offers essentially the same
(or better) benefits as those provided for in the Relocation Policy
in effect as of January 1, 2009), (I) reimbursement for reasonable moving expenses actually
incurred by the Employee in relocating back to the
Chicago, Illinois area, such reimbursement to be made by
Atlas no later than the end of the third year following the
year in which the Employment Period terminates, and (II) tax gross-up payments that reimburse the Employee for
any income taxes that the Employee incurs as a result of the
reimbursements made by Atlas under the preceding clause (I), with any such gross-up payment to be made by Atlas no
later than the end of the year following the year in which
the Employee remits the income taxes that are being
grossed up by the applicable payment; and
	 
	 	(iii)	 	continued coverage for a period of twelve months
immediately following the date on which the Employment Period
terminates under the health (medical, dental, and vision) and life
insurance programs of Atlas (or, if continued coverage under such
Atlas programs is not available or practicable, then receive coverage
under substantially similar individual health and life insurance
policies for such twelve-month period); provided that such coverage
will cease immediately in the event the Employee obtains comparable
coverage in connection with subsequent employment.

     7. Section 4.2(b) of the Employment Agreement is amended in its entirety to read as follows:

     “(b) Upon the death or Permanent Disability of the Employee during the
Employment Period, the Employment Period shall terminate and the Employee’s Base
Annual Salary that is accrued for the then-current pay period but unpaid as of the
date of such death or Permanent Disability shall be paid to the Employee or the
Employee’s personal representative, as applicable. In addition, upon the Permanent
Disability

3

 

of the Employee, the Employee shall be entitled to the compensation, relocation
benefits, and benefit coverage set forth in Section 4.2(a) above. Further, upon
the death of the Employee, the Employee’s spouse or estate shall be entitled to
the compensation and relocation benefits set forth in Sections 4.2(a)(i) and
4.2(a)(ii) above, with the amount under Section 4.2(a)(i) above to be paid by
Atlas within ten (10) days immediately following the Employee’s date of death, and
the Employee’s spouse and covered dependents shall be entitled to the benefit
coverage set forth in Section 4.2(a)(iii) above.

     8. The third sentence of Section 4.2(d)(iii) of the Employment Agreement is
deleted in its entirety.

     9. A new Section 4.2(d)(iv) is added to the Employment Agreement to read
as follows:

     “(iv) If a reduction is made pursuant to subparagraph (i), such reduction
will be made, first, to any post-employment lump-sum payment being made to the
Employee under Sections 4.2(a) or 4.2(b) above, or Section 4.2(e) below, and
second, if further reductions are still required, to any post-employment benefit
coverage being provided to the Employee under such Sections.”

     10. A new Section 4.2(e) is added to the Employment Agreement to read as
follows:

     “(e) (i) If, within the twelve-month period immediately following a Change of
Control, the Employment Period is terminated by Atlas for reasons other than Cause
or if the Employment Period is terminated by the Employee for Good Reason, and
subject to the Employee’s execution of a general release upon terms and conditions
consistent with this Agreement and acceptable to Atlas and Employee, which release
must be presented to Employee upon or promptly after termination of the Employment
Period, fully executed and become effective before the six-month anniversary of
the date on which the Employment Period terminates, then the Employee shall be
entitled to (and not in addition to) the compensation, relocation benefits, and
benefit coverage set forth in Section 4.2(a) above, except that the amount of the
lump-sum payment under Section 4.2(a)(i) above shall be equal to twenty four (24)
months of the Employee’s then-current monthly Base Salary.

4

 

     (ii) If, within the six-month period immediately following a termination of
the Employment Period by Atlas for reasons other than Cause or by the Employee for
Good Reason, a Change of Control occurs, then, in addition to the lump-sum payment
set forth in Section 4.2(a)(i) above, the Employee shall receive a lump-sum
payment on the Lump-Sum Payment Date equal to six (6) months of the Employee’s
then-current monthly Base Salary.”

     11. A
new Section 4.2(f) is added to the Employment Agreement to read as
follows:

     “(f) Notwithstanding any other provision of this Agreement to the contrary,
because the Employee is a “specified employee” (as that term is defined in Section
409A), to the extent that any payment or benefit under this Agreement constitutes
an amount payable or benefit to be provided under a “nonqualified deferred
compensation plan” (as defined in Section 409A) upon or as a result of a
“separation from service” (as defined in Section 409A) and which is not exempt
from Section 409A, then, notwithstanding any other provision in this Agreement to
the contrary, such payment or benefit provision will not be made to the Employee
during the six-month period immediately following his “separation from service”
date. Instead, on the first day of the seventh month following such “separation
from service” date, all amounts that otherwise would have been paid or provided to
the Employee during that six-month period, but were not because of this provision,
will be paid or provided to the Employee, with any cash payment delayed during
such six-month period to be made to the Employee in a single lump sum.”

     12. The title of Section 5.3
(“Arbitration”) of the Employment Agreement
should be deleted in its entirety and replaced with the title
“Disputes,” In addition, the
penultimate sentence of the last paragraph of Section 5.3 of the Employment Agreement
is deleted in its entirety and replaced with the following six sentences:

     “In any legal proceedings relating to this Agreement, the Parties shall
equally divide all costs and expenses incurred in such proceeding and related legal
proceedings; provided, however, that the Employee shall, if successful, be entitled
to recover all of his costs and expenses (including attorneys’ fees). Any amount
payable by Atlas pursuant to the immediately preceding sentence will be paid as
follows: (i) if the dispute has not been resolved by the end of any calendar year
subsequent to the time that a proceeding relating to such dispute has been
commenced, then Atlas shall reimburse the Employee by no later than December 31 of
the

5

 

following calendar year for all costs and expenses (including attorneys’ fees)
incurred by the Employee during such calendar year for such proceeding, provided
that the Employee will be required to repay such amounts promptly to Atlas upon
the resolution of such dispute unless he is successful as to such dispute; and
(ii) upon resolution of the dispute, Atlas shall reimburse the Employee by no
later than December 31 of the calendar year following the year in which such
resolution occurs for all costs and expenses (including attorneys’ fees) incurred
by the Employee for such proceeding during the calendar year in which such
resolution occurs, but only if the Employee is successful as to such dispute.
Notwithstanding the foregoing, in no event will the Employee be reimbursed for any
costs or expenses under clauses (i) or (ii) of the immediately preceding sentence
later than sixty (60) days after the dispute has been resolved. The reimbursement
right set forth in this paragraph shall be limited, to costs and expenses
(including attorneys’ fees) incurred during the Employee’s employment with Atlas
and during the ten-year period immediately thereafter. Any amount paid by Atlas in
any year under this paragraph will not be affected by the amount of any payment
made by Atlas pursuant to this paragraph in any other year, and under no
circumstances will the Employee by permitted to liquidate or exchange the benefit
afforded him in this paragraph for cash or any other benefit. This benefit is
subject to the limitations set forth in Section 4.2(f) above.”

     13. Continued Validity of the Employment Agreement. Except as amended
and superseded by this Amendment, the Employment Agreement will remain in full force
and effect, will continue to bind the parties hereto, and will continue to govern the terms
and conditions of the Employee’s continued employment with Atlas. To the extent that
the terms of this Amendment conflict or are inconsistent with the terms of the
Employment Agreement, the terms of this Amendment will govern.

     14. Amendment Effective Date. This Amendment will become binding and
effective on December 31, 2008.

     15. Governing Law. This Amendment will be governed by and construed in
accordance with the laws of the State of New York, without reference to principles of
conflict of law.

     16. Counterparts. This Amendment may be executed in several counterparts,
each of which will be deemed to be an original, and all such counterparts when taken
together will constitute one and the same original.

[SIGNATURE PAGE FOLLOWS]

6

 

IN WITNESS WHEREOF, the parties hereto have executed this Amendment to your Employment Agreement
dated September 8, 2006, on the day and year first written above, to be effective as of December
31, 2008.

	 	 	 	 	 	 	 
	ATLAS AIR, INC.	 	JOHN W. DIETRICH	 	 
	 
	 	 	 	 	 	 
	By:

	 	/s/ Adam R. Kokas
 

	 	/s/ John W. Dietrich
 
	 	 
	Name: Adam R. Kokas	 	 	 	 
	Title:   Senior Vice President,	 	 	 	 
	 
	 	    General Counsel, Chief Human	 	 	 	 
	 
	 	    Resources Officer & Secretary	 	 	 	 

7

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