EX-4.1



 Exhibit 4.1 

THIS INSTRUMENT OF RESIGNATION, APPOINTMENT AND ACCEPTANCE (this “Instrument”), dated as of June 6, 2016
(“Effective Date”), is by and among Atlas Resource Partners Holdings, LLC, a Delaware limited liability company (the “Company”), Atlas Resource Finance Corporation, a Delaware corporation (together with the Company,
the “Issuers”), Atlas Resource Partners, L.P. (the “Parent Guarantor”), the Subsidiary Guarantors named herein (the Parent Guarantor and Subsidiary Guarantors hereinafter known as the “Guarantors”), Wells Fargo
Bank, National Association, a national banking association duly organized and existing under the laws of the United States of America (the “Resigning Trustee”), and U.S. Bank National Association, a national banking association duly
organized and existing under the laws of the United States of America (the “Successor Trustee”). Capitalized terms not otherwise defined herein shall have the same meaning ascribed to such terms in the Indenture (as defined below).

 RECITALS 

WHEREAS, the Issuers, the Guarantors and the Resigning Trustee are party to an Indenture dated as of July 30, 2013, (as the same may be
supplemented and amended from time to time, the “Indenture”); 
 WHEREAS, pursuant to the Indenture, on July 30, 2013
and October 14, 2014, the Issuers (or their predecessor) issued $250,000,000.00 and $75,000,000.00 of principal amount, respectively, for an aggregate of $325,000,000.00 in principal amount of their 9.25% Senior Notes due 2021 (the
“Notes”), which are issued in the form of global notes registered in the name of CEDE & CO., nominee of The Depository Trust Company (the “Global Notes”); 

WHEREAS, the Issuers appointed the Resigning Trustee as the Trustee, Note Custodian, Registrar and Paying Agent under the Indenture;

 WHEREAS, there is presently issued and outstanding $312,935,000.00 in aggregate principal amount of Notes; 

WHEREAS, Section 7.08 of the Indenture provides that the Trustee may at any time resign by giving written notice of such resignation to
the Issuers; 
 WHEREAS, Section 7.08 of the Indenture provides that if the Trustee resigns, the Issuers shall promptly appoint a
successor Trustee; 
 WHEREAS, the Resigning Trustee desires to resign as Trustee, Note Custodian, Registrar and Paying Agent under the
Indenture, and the Issuers desire to appoint the Successor Trustee as Trustee, Note Custodian, Registrar and Paying Agent under the Indenture to succeed the Resigning Trustee in each of such capacities under the Indenture; and 







 WHEREAS, the Successor Trustee is willing to accept the appointment as Trustee, Note Custodian,
Registrar and Paying Agent under the Indenture; 
 NOW, THEREFORE, in consideration of the covenants herein and other good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows: 
 1. Acceptance
of Resignation of Resigning Trustee; Appointment of Successor Trustee. The Resigning Trustee hereby resigns as Trustee, Note Custodian, Registrar and Paying Agent under the Indenture. The Issuers accept the resignation of the Resigning
Trustee as Trustee, Note Custodian, Registrar and Paying Agent under the Indenture. The Issuers hereby appoint the Successor Trustee as Trustee, Note Custodian, Registrar and Paying Agent under the Indenture. The Issuers hereby acknowledge that, as
of the Effective Date, the Successor Trustee shall be the Trustee under the Indenture and shall hold all rights, powers, duties and obligations which the Resigning Trustee now holds under and by virtue of the Indenture as Trustee, Note Custodian,
Registrar and Paying Agent under the Indenture. The Issuers shall execute and deliver such further instruments and shall do such other things as the Successor Trustee may reasonably require so as to more fully and certainly vest in and confirm to
the Successor Trustee all the rights, powers, duties and obligations hereby assigned, transferred, delivered and confirmed to the Successor Trustee as Trustee, Note Custodian, Registrar and Paying Agent under the Indenture. 

2. Issuers’ Representations and Warranties. The Issuers each represent and warrant to the Successor Trustee that:

  

	 	a.	It is duly organized and validly existing under the laws of the State of Delaware; 

  

	 	b.	It has full power, authority, and right to execute, deliver and perform this Instrument; 

  

	 	c.	The Indenture was validly and lawfully executed and delivered by the Issuers and the Guarantors and is in full force and effect. The current outstanding aggregate principal amount of the Notes is $312,935,000.00;


  

	 	d.	There is no action, suit or proceeding pending or, to the best of the Issuers’ knowledge, threatened against the Issuers before any court or any governmental authority arising out of any act or omission of the
Issuers under the Indenture; 

  

	 	e.	No covenant or condition contained in the Indenture has been waived by the Issuers or, to the best of the Issuers’ knowledge, by holders of the percentage in aggregate principal amount of the Notes required to
effect any such waiver; 









	 	f.	Assuming the accuracy of the representation made by the Successor Trustee in Section 4 hereof, all conditions precedent relating to the appointment of the Successor Trustee as Trustee, Note Custodian, Registrar and
Paying Agent under the Indenture have been complied with by the Issuers, and such appointment is permitted by the Indenture; 

  

	 	g.	No event has occurred and is continuing which is, or after notice or lapse of time would become, an Event of Default under the Indenture; and 


 

	 	h.	Except as set forth on Exhibit B hereto, the Indenture has not been supplemented and remains in full force and effect. 


3. Resigning Trustee Representations and Warranties. The Resigning Trustee hereby represents and warrants to the
Successor Trustee that: 
  

	 	a.	To the knowledge of the responsible officer of the Resigning Trustee who is signing this document, no covenant or condition contained in the Indenture has been waived by the Resigning Trustee or by the holders of the
percentage in aggregate principal amount of Notes required by the Indenture to effect any such waiver; 

  

	 	b.	To the knowledge of the responsible officer of the Resigning Trustee who is signing this document, there is no action, suit or proceeding pending or threatened against the Resigning Trustee before any court or
governmental authority arising out of any action or omission by the Resigning Trustee as Trustee, Note Custodian, Registrar or Paying Agent under the Indenture; 

  

	 	c.	The Resigning Trustee shall endeavor to deliver to Successor Trustee, as of or immediately after the Effective Date, to the extent available, all of the documents listed in Exhibit B hereto; 


 

	 	d.	The execution and delivery of this Instrument has been duly authorized by the Resigning Trustee, and this Instrument constitutes the Resigning Trustee’s legal, valid, binding and enforceable obligation;


  

	 	e.	The Resigning Trustee certifies that $312,935,000.00 in principal amount of Notes is outstanding and interest due on the Notes has been paid to, and including, February 15, 2016; and 


 

	 	f.	Except as set forth on Exhibit B hereto, the Indenture has not been supplemented and remains in full force and effect. 








 4. Successor Trustee Representation and Warranty. The
Successor Trustee represents and warrants to the Resigning Trustee and the Issuers that it is eligible to serve as Trustee under Section 7.10 of the Indenture. This Instrument has been duly authorized, executed and delivered on behalf of the
Successor Trustee and constitutes its legal, valid and binding obligation, enforceable in accordance with its terms. 
 5.
Assignment by Resigning Trustee. Effective on the Effective Date, the Resigning Trustee hereby confirms, assigns, transfers, delivers and conveys to the Successor Trustee, as Trustee, Note Custodian, Registrar and Paying Agent
under the Indenture, all rights, powers, duties and obligations which the Resigning Trustee now holds under and by virtue of the Indenture as Trustee, Note Custodian, Registrar and Paying Agent, and effective as of such date does hereby pay over to
the Successor Trustee any and all property and moneys held by the Resigning Trustee under and by virtue of the Indenture. 
 6.
Acceptance by Successor Trustee. The Successor Trustee accepts its appointment as Trustee, Note Custodian, Registrar and Paying Agent under the Indenture and shall assume said rights, powers, duties and obligations upon the
terms and conditions set forth in the Indenture. Promptly after the execution and delivery of this Instrument, the Successor Trustee shall cause a notice, the form of which is annexed hereto as Exhibit A, to be sent to the Issuers and each
Holder of the Notes. 
 7. Additional Documentation. The Resigning Trustee, for the purposes of more fully and
certainly vesting in and confirming to the Successor Trustee the rights, powers, duties and obligations hereby assigned, transferred, delivered and conveyed, agrees, upon reasonable request of the Successor Trustee, to execute, acknowledge and
deliver such further instruments of conveyance and further assurance and to do such other things as may reasonably be required by the Successor Trustee. 

8. Choice of Laws. This Instrument shall be governed by the laws of the State of New York. 

9. Counterparts. This Instrument may be executed in any number of counterparts, each of which, when so executed and
delivered, shall be deemed an original, but all counterparts shall constitute but one Instrument. Delivery of a counterpart hereof by facsimile transmission or by e-mail transmission of a portable document format file (also known as a
“PDF” file) shall be effective as delivery of a manually executed counterpart hereof. 
 10. Patriot Act. The
Issuers acknowledge that, in accordance with Section 326 of the USA Patriot Act, the Successor Trustee, like all financial institutions, is required to obtain, verify, and record information that identifies each person or legal entity that
establishes a relationship or opens an account with the Successor Trustee. The Issuers agree that they will provide the Successor Trustee with such information as it may reasonably request in order for it to satisfy the requirements of the USA
Patriot Act. 







 11. Notices. All notices, whether faxed or mailed, will be deemed received
in accordance with Section 12.02 of the Indenture to the following: 
 TO THE SUCCESSOR TRUSTEE: 

U.S. Bank National Association 

Global Corporate Trust Services 

5555 San Felipe, Suite 1150 

Houston, Texas 77056 
 Attn:
Steven Finklea, Vice President 
 Facsimile: 713-235-9213 

TO THE RESIGNING TRUSTEE: 
 Wells Fargo Bank,
National Association 
 150 East 42nd Street, 40th Floor 
 New York, New York 10017 

Attention: Corporate Trust Services – Administrator for Atlas Resources 

                        
                                         
   Finance Corporation 
 Facsimile: 917-260-1593 

TO THE ISSUERS: 
 Atlas Resource Partners
Holdings, LLC 
 712 Fifth Avenue, 11th Floor 

New York, New York 10019 

Attention: Betsy Toney 

Facsimile: 215-561-5692 
 With a copy to: 

Paul Hastings 
 600 Travis Street

 58th Floor 

Houston, Texas 77002 
 Attention:
Lindsay Sparks 
 Facsimile: 713-353-3100 

12. Effectiveness. This Instrument and the resignation, appointment and acceptance effected hereby shall be effective as
of the close of business on the Effective Date, upon the execution and delivery hereof by each of the parties hereto; provided, that the resignation of the Resigning Trustee as Note Custodian, Registrar and Paying Agent and the appointment of
the Successor Trustee as Note Custodian, Registrar and Paying Agent under the Indenture shall be effective 10 business days after the Effective Date. 







 [Remainder of page left intentionally blank] 







 IN WITNESS WHEREOF, the parties hereto have executed this Instrument as of the date set
forth above. 
  

			
	Atlas Resource Partners Holdings, LLC, as Issuer
		
	By	 	 /s/ Jeffrey M. Slotterback

	Name: Jeffrey Slotterback
	Title: Chief Financial Officer
	
	Atlas Resource Finance Corporation, as Issuer
		
	By	 	 /s/ Jeffrey M. Slotterback

	Name: Jeffrey Slotterback
	  Its: Chief Financial Officer
	
	Parent Guarantor:
	Atlas Resource Partners, L.P.
	By: Atlas Energy Group, LLC, its General Partner
		
	By	 	 /s/ Jeffrey M. Slotterback

	Name: Jeffrey Slotterback
	Title: Chief Financial Officer

 Subsidiary Guarantors: 

Atlas Energy Colorado, LLC 

Atlas Energy Indiana, LLC 

Atlas Energy Ohio, LLC 

Atlas Energy Tennessee, LLC 

Atlas Noble, LLC 
 Atlas
Resources, LLC 
 REI-NY, LLC 

Resource energy, LLC 

Resource Well Services, LLC 

Viking Resources, LLC 

ARP Barnett, LLC 
 ARP
Oklahoma, LLC 
 Atlas Barnett, LLC 

ARP Production Company, LLC 

ARP Mountaineer Production, LLC 

ARP Production Company, LLC 

ARP Rangely Production, LLC 
  

			
	By	 	 /s/ Jeffrey M. Slotterback

	 Name: Jeffrey Slotterback

	 Title: Chief Financial Officer










					
		 	ARP Eagle Ford, LLC


        By: Atlas Resource Partners Holdings, LLC, its Sole Member 

					
			
		 	By	 	 /s/ Jeffrey M. Slotterback

		 	Name: Jeffrey Slotterback
		 	Title: Chief Financial Officer
		
		 	ATLS Production Company, LLC


        By: ARP Production Company, LLC, its Sole Member 

        By: Atlas Resource Partners Holdings, LLC, its Sole Member 

					
			
		 	By	 	 /s/ Jeffrey M. Slotterback

		 	Name: Jeffrey Slotterback
		 	Title: Chief Financial Officer
		
		 	ARP Barnett Pipeline, LLC
		
		 	By: ARP Barnett, LLC, its Sole Member


        By: Atlas Resource Partners Holdings, LLC, its Sole Member 

					
			
		 	By	 	 /s/ Jeffrey M. Slotterback

		 	Name: Jeffrey Slotterback
		 	Title: Chief Financial Officer

 Wells Fargo Bank, National Association, as Resigning Trustee 

 

			
	By	 	 /s/ Martin Reed

	Name: Martin Reed
	  Its    Vice President

 U.S. Bank
National Association, as Successor Trustee 

			
		
	By	 	 /s/ Steven A. Finklea

	Name: Steven A. Finklea
	  Its    Vice President








 EXHIBIT A 

[U.S. Bank Letterhead] 
 Notice
to Holders of Atlas Resource Partners Holdings, LLC and Atlas Resource Finance Corporation (the “Issuers”) 9.25% Senior Notes due 2021 (the “Notes”): 

Cusip Numbers1: 049296AE6 

THIS NOTICE CONTAINS IMPORTANT INFORMATION THAT IS OF INTEREST TO THE REGISTERED AND BENEFICIAL HOLDERS OF THE SUBJECT NOTES. IF APPLICABLE, ALL
DEPOSITORIES, CUSTODIANS, AND OTHER INTERMEDIARIES RECEIVING THIS NOTICE ARE REQUESTED TO EXPEDITE RE-TRANSMITTAL TO BENEFICIAL OWNERS OF THE NOTES IN A TIMELY MANNER. 

Reference is hereby made to that certain Indenture, dated as of July 30, 2013 (as supplemented, modified or amended from time to time,
the “Indenture”), by and among the Issuers, each of the Guarantors named in the Indenture, and Wells Fargo Bank, National Association, as Trustee, pursuant to which the above-referenced Notes were issued and are outstanding. 

NOTICE IS HEREBY GIVEN, pursuant to Section 7.08 of the Indenture that Wells Fargo Bank, National Association has resigned as Trustee,
Note Custodian, Registrar and Paying Agent under the Indenture. 
 NOTICE IS HEREBY FURTHER GIVEN, pursuant to Section 7.08 of the
Indenture, that the Issuers have appointed U.S. Bank National Association (“U.S. Bank”), whose corporate trust office is located at 5555 San Felipe, Suite 1150, Houston, Texas 77056, as Successor Trustee, Note Custodian, Registrar and
Paying Agent under the Indenture, and U.S. Bank has accepted such appointment. 
 NOTICE IS HEREBY FURTHER GIVEN that Wells Fargo Bank,
National Association’s resignation as Trustee and U.S. Bank’s appointment as Successor Trustee will be effective as of the closing of business on June 6, 2016. 

Dated: June 2, 2016 
 U.S. Bank National
Association, 
 as Successor Trustee 

 

	1 	CUSIP numbers appearing herein have been included solely for the convenience of the Holders. The Trustee assumes no responsibility for the selection or use of such numbers and makes no representation as to the
correctness of the CUSIP numbers listed above. 








 EXHIBIT B 

Documents to be delivered by Resigning Trustee to Successor Trustee as to the Indenture: 

1. Executed copy of the Indenture, including executed copies of the 1st Supplemental
Indenture dated July 31, 2013, the Second Supplemental Indenture dated October 14, 2014, the Third Supplemental Indenture dated July 23, 2015 and the Fourth Supplemental Indenture dated December 17, 2015. 

2. Certified list of noteholders as of the Effective Date, certificate detail and all “stop transfers” and the reason for such
“stop transfers” (or, alternatively, if there are a substantial number of registered noteholders, the computer tape reflecting the identity of such noteholders). 

3. Copies of any official notices sent by the Resigning Trustee to all the holders of the Notes pursuant to the terms of the Indenture during
the past twelve months and a copy of the Resigning Trustee’s most recent annual report to Holders, if any. 
 4. Original Global Notes.

 5. LIST OTHER ITEMS NEEDED FOR ADMINISTRATION AS MAY BE REQUIRED 

6. Such other non-confidential, unprivileged documents or information as the Successor Trustee may reasonably request on or after the
Effective Date.