Document:

EX-10.6

 Exhibit 10.6 

FIRST AMENDMENT 
 TO

 SECOND AMENDED AND RESTATED 

REFINED PRODUCT PIPELINES AND TERMINALS AGREEMENT 

This First Amendment to Second Amended and Restated Refined Product Pipelines and Terminals Agreement (this “Amendment”) is
dated as of October 29, 2018, to be effective as of June 4, 2018 (the “Effective Time”) by and between HOLLYFRONTIER REFINING & MARKETING LLC (“HFRM”) and HOLLY ENERGY PARTNERS-OPERATING, L.P.
(“HEP Operating”). Each of HFRM and HEP Operating are collectively referred to herein as the “Parties.” 

WHEREAS, the Parties desire to amend certain provisions of the Second Amended and Restated Refined Product Pipelines and Terminals Agreement,
dated as of February 22, 2016, by and between HFRM and HEP Operating (the “Agreement”) as set forth herein. 
 NOW,
THEREFORE, in consideration of the covenants and obligations contained herein, the Parties hereby agree as follows: 
 ARTICLE 1 

AMENDMENTS 
 1.1 Section
2(n). Section 2(n) of the Agreement is hereby amended by deleting it in its entirety and replacing it with the following: 

“Terminal Access Agreement. HFRM agrees to use its commercially reasonable efforts to enter into a terminal access agreement with
any third party that uses any terminal owned by HEP Operating or its Affiliates where HFRM is the sole customer. 
 1.2 Amendment to
Exhibit B. Exhibit B to the Agreement is hereby deleted and replaced in its entirety with Exhibit B attached to this Amendment. 

1.3 Amendment to Exhibit C. Exhibit C to the Agreement is hereby deleted and replaced in its entirety with Exhibit C
attached to this Amendment. 
 1.4 Amendment to Exhibit C-1. Exhibit C-1 to the Agreement is hereby deleted and replaced in its entirety with Exhibit C-1 attached to this Amendment. 

ARTICLE 2 
 MISCELLANEOUS

 2.1 Remainder of Agreement. Except as expressly set forth herein, this Amendment shall not by implication or otherwise alter,
modify, amend or in any way affect any of the terms, conditions, obligations, covenants or agreements contained in the Agreement, all of which shall continue to be in full force and effect. Unless the context otherwise requires, after the execution
and delivery hereof, any reference in the Agreement to “this Agreement” shall mean the Agreement as amended hereby. 
 2.2
Counterparts. This Amendment may be executed in counterparts each of which shall be deemed an original. An executed counterpart of this Amendment transmitted by facsimile shall be equally as effective as a manually executed counterpart. 

 2.3 Entire Agreement. The Agreement, as amended by this Amendment, contains the
entire agreement between the Parties as to the subject matter of the Agreement and, except as provided for in this Amendment, the terms and provisions of the Agreement shall remain in full force and effect as originally written. 

[Remainder of page intentionally left blank. Signature pages follow.] 

 IN WITNESS WHEREOF, the undersigned Parties have executed this Amendment as of the date
first written above to be effective as of the Effective Time. 
  

			
	HEP OPERATING:
	
	Holly Energy Partners-Operating, L.P.
		
	By:	 	 /s/ Richard L. Voliva III

	Name:	 	Richard L. Voliva III
	Title:	 	Executive Vice President & Chief Financial Officer
	
	HFRM:
	
	HollyFrontier Refining & Marketing LLC
		
	By:	 	 /s/ Thomas G. Creery

	Name:	 	Thomas G. Creery
	Title:	 	Chief Executive Officer and President

 [Signature Page to First Amendment to Second Amended and Restated Refined Product Pipelines and
Terminals Agreement] 

 EXHIBIT B 

REFINED PRODUCT TERMINALS 

As of February 1, 2016 
  

													
	 Terminal Location
	  	Storage
Capacity
(barrels)	 	  	Number
of
Tanks	 	  	 Supply
Source
	  	Mode of Delivery
	 Moriarty, NM
	  	 	189,000	 	  	 	9	 	  	Pipeline	  	Truck
	 Bloomfield, NM
	  	 	193,000	 	  	 	7	 	  	Pipeline	  	Truck
	 Mountain Home, ID(1)
	  	 	120,000	 	  	 	3	 	  	Pipeline	  	Pipeline
	 Spokane, WA
	  	 	333,000	 	  	 	32	 	  	Pipeline/Rail	  	Truck
	 Artesia facility truck rack
	  	 	N/A	 	  	 	N/A	 	  	Refinery	  	Truck
	 Woods Cross facilities
	  	 	N/A	 	  	 	N/A	 	  	Refinery	  	Truck/Pipeline
		  	  
	  
	 	  				  		  	
	 Total
	  	 	835,000	 	  				  		  	
		  	  
	  
	 	  				  		  	

  
  

	(1)	 Handles only jet fuel. 

 EXHIBIT C 

FEE SCHEDULE 
 As of
July 1, 2018 
  

	1.	 HFRM will pay a terminal service fee of $0.3752 per barrel for truck rack deliveries and $0.1251 per barrel for
pipeline pump-over deliveries at each of the Refined Product Terminals, except that HFRM will pay $0.1382 per barrel for pipeline pump-over deliveries at the El Paso Hawkins Terminal. 

 

	2.	 HFRM will receive a discount of $0.1152 per barrel for truck rack deliveries at the Moriarty, New Mexico
terminal that exceed the Monthly Average Base Volume. 

  

	3.	 HFRM will pay a service fee of $0.3126 per barrel for truck rack deliveries for facilities located within the
Refineries. 

  

	4.	 HFRM will pay a handling fee of $0.6563 per barrel for the movement of isobutane, propane and normal butane
within any of the Refined Product Terminals. 

  

	5.	 HFRM will pay a fee for lubricity additive injections to diesel fuel products, gasoline additive injections,
red dye additive injections to diesel fuel products and ethanol injections made at the Refined Product Terminals. The fees for such injections, as well as the party responsible for supplying such additives, are set forth in the chart attached hereto
as Exhibit C-1. The Parties agree and understand that the fees set forth on Exhibit C-1 are subject to change based on changes in cost of such additives.

  

	6.	 HFRM will supply, at its sole cost and expense, all clay and/or clay filters used in the clay filtration
systems at the El Paso Hawkins Terminal. 

  

	7.	 Each of the service fees listed on this Exhibit C will adjust at the beginning of each Contract Year by
a percentage equal to the percentage change in the service fee in effect at the end of each of the two preceding Contract Years in the index comprised of comparable fees posted by Kinder Morgan at its Phoenix and Las Vegas terminals;
provided, however, that no adjustment shall be made which would result in a decrease in any service fee. 

 EXHIBIT C-1 

SCHEDULE OF ADDITIVE FEES 
  

																			
	 Terminal Name
	  	 	 	  	Red Dye
Additive Inj
Fee?
per bbl	  	Gasoline
Additive
Inj Fee?
per bbl	  	Lubricity
Additive Inj
Fee?
per bbl	  	Ethanol
Injection
Fee?	  	HFRM
Supplies
Red Dye	  	HFRM
Supplies
Gasoline
Additive	  	HFRM
Supplies
Lubricity
Additive
	 El Paso Hawkins Terminal
	  	 	HFRM shipper	 	  	No	  	No	  	$0.1692	  	No	  	Yes	  	Yes	  	No
	 Artesia Rack
	  	 	HFRM shipper	 	  	$0.2418	  	No	  	No	  	No	  	No	  	Yes	  	Yes
	 Moriarty Terminal
	  	 	HFRM shipper	 	  	No	  	No	  	$0.0581	  	No	  	Yes	  	Yes	  	Yes
	 Bloomfield Terminal
	  	 	HFRM shipper	 	  	No	  	No	  	Inactive	  	No	  	Yes	  	Yes	  	Yes
	 Spokane Terminal
	  	 	HFRM shipper	 	  	$0.0301	  	$0.0409	  	$0.1692	  	No	  	No	  	No	  	No
	 Woods Cross Terminal
	  	 	HFRM shipper	 	  	$0.0581	  	No	  	0.0581	  	No	  	Yes	  	No	  	NoEX-10.7

 Exhibit 10.7 

SECOND AMENDMENT 
 TO

 AMENDED AND RESTATED MASTER TOLLING AGREEMENT 

(Operating Assets) 
 THIS
SECOND AMENDMENT TO AMENDED AND RESTATED MASTER TOLLING AGREEMENT (Operating Assets) (this “Amendment”) is entered into as of October 29, 2018 by and among the Persons set forth on Exhibit A (each hereinafter sometimes
referred to as a “Party” and sometimes collectively referred to as the “Parties”). 
 RECITALS: 

A. Effective as of October 1, 2016, the Parties entered into a certain Amended and Restated Master Tolling Agreement (Operating Assets)
(as amended by the Amendment to Amended and Restated Master Tolling Agreement, dated January 1, 2017, the “Amended and Restated Master Tolling Agreement”). Capitalized terms used but not otherwise defined in this Amendment have
the meanings ascribed to such terms in the Amended and Restated Master Tolling Agreement. 
 B. Exhibit
C-1 to the Amended and Restated Master Tolling Agreement provides for the adjustment of the Tolling Fee based on the OPEX and CAPEX actually incurred during the initial four (4) Contract Quarters of
the Term. 
 C. The Parties desire to adjust the Tolling Fee for the Woods Cross Assets as provided in Exhibit C-1 attached to the Amended and Restated Master Tolling Agreement, on the terms and conditions set forth herein. 

AGREEMENT: 
 NOW,
THEREFORE, in consideration of the premises and the covenants and agreements set forth herein, and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Parties hereby amend the Amended and
Restated Master Tolling Agreement as follows: 
 1. Incorporation of Recitals. The recitals for this Amendment are fully incorporated
herein by the reference thereto with the same force and effect as though recited herein. 
 2. Amendment to Exhibit C. Effective as of
12:01 a.m. Central Time on October 1, 2017, Exhibit C-1 attached to the Amended and Restated Master Tolling Agreement is hereby deleted and replaced, in its entirety, with Exhibit C-2 attached to this Amendment. 
 3. Counterparts. This Amendment may be executed in
counterparts each of which shall be deemed an original. An executed counterpart of this Amendment transmitted by facsimile shall be equally as effective as a manually executed counterpart. 

4. Successors and Assigns. This Amendment shall inure for the benefit of and shall be binding on each of the Parties and their
respective successors and/or assigns. 
 5. Entire Agreement. This Amendment contains the entire agreement between the Parties as to
the subject matter hereof and, except as provided for in this Amendment, the terms and provisions of the Amended and Restated Master Tolling Agreement shall remain in full force and effect. 

[Signature page follows] 

 IN WITNESS WHEREOF, the Parties have caused this Amendment to be executed by their duly
authorized officers to be effective as of the date first set forth above. 
  

			
	HEP OPERATING:
	
	Holly Energy Partners—Operating, L.P.
		
	By:	 	 /s/ Richard L. Voliva III

		 	Richard L. Voliva III
		 	Executive Vice President and CFO
	
	APPLICABLE REFINERY OWNER:
	
	HollyFrontier El Dorado Refining LLC
	HollyFrontier Woods Cross Refining LLC
		
	By:	 	 /s/ Thomas G. Creery

		 	Thomas G. Creery
		 	Senior Vice President, Commercial

  
 2 

 Exhibit A 

to 
 Amended and Restated
Master Tolling Agreement 
  
  

Parties: 
 HollyFrontier El Dorado and HEP Operating, as to the
El Dorado Assets. 
 HollyFrontier Woods Cross and HEP Operating, as to the Woods Cross Assets. 

  
 Exhibit A-1 

 Exhibit C-2 

to 
 Amended and Restated
Master Tolling Agreement 
  
  

Applicable Assets; Minimum Throughput Commitment; Tolling Fees and Adjustments; Applicable Term 

 

																									
	 Appli-
cable
Assets
	  	Type of
Applicable
Asset	  	Products	  	Minimum
Throughput
Commit-
ment (on a
BPD basis)	  	Tolling
Fee*	  	Tolling Fee
Adjustment	  	PPI
Adjust-
ment
Minimum/
Cap	  	Fee
Adjustment
Commence-
ment Date	  	Purchase
Price	  	Accrued
Turn-
around
Cost	  	Assumed
Fuel Gas
Cost	  	Initial Term
(all times are
Dallas, TX
time)	  	Extension Term
(all times are Dallas,
TX time)
	 El Dorado
 Assets
	  	Naphtha
Fractiona-
tion Unit	  	Isopentane1  

ISOM
Feed
  

Int.
Naphtha
  

Reformer
 Feed
	  	48,750
BPD	  	$0.4020/BBL2	  	PPI/HFC
 Merit CompAdjustment3

 
 Turnaround
Surcharge4

 
 Fuel Gas
Surcharge5
	  	Subject
to 1%
Minimum/
3% Cap3	  	July 1,
2017	  	$25,936,371	  	$1.6M4	  	$73,6105	  	12:01 a.m.
on
November 1,
2015 (the
“Effective
Time”) to
12:00
mid-night on
October 31,
2030	  	The Applicable Refinery
Owner shall have the
option to extend the
Applicable Term
beyond the Initial Term
for one additional five
(5) year period
beginning at 12:01 am
on November 1,
2030
and ending at 12:00
midnight on October 31,
2035 on the same terms
and conditions as in
existence for the Initial
Term.

  
 Exhibit C2-1 

																																	
	 Appli-
cable
Assets
	  	Type of
Applicable
Asset	  	Products	  	Minimum
Throughput
Commit-
ment (on a
BPD basis)	 	Tolling
Fee*	 	 	Tolling Fee
Adjustment	 	PPI
Adjust-
ment
Minimum/
Cap	  	Fee
Adjustment
Commence-
ment Date	  	Purchase
Price	 	  	Accrued
Turn-
around
Cost	 	 	Assumed
Fuel Gas
Cost	 	  	Initial
Term (all
times are
Dallas,
TX time)	 	Extension Term (all
times are Dallas, TX
time)
	 Woods Cross Assets
	  	Crude Unit 2	  	Naphtha
 Diesel
 tower

bottoms
	  	14,625
BPD6	 	$	2.7015/BBL	8  	 	PPI/WX
Union
Annual
Increase7  

Turn-
around
Surcharge4
  

Fuel Gas
Surcharge
(excluding
Polymeri-zation
Unit)5
	 	None	  	July 1,
2017	  	$	64.75M	 	  	$	8.7M	4  	 	$	11,871	 	  	12:01 a.m.
on
October 1,
2016
(the
“Effective
Time”)
to
12:00
midnight
on
September 30,
2031	 	The Applicable Refinery
Owner shall have the
option to extend the
Applicable Term
beyond the Initial
Term for one
additional five
(5) year period
beginning at 12:01
am on
October 1,
2031 and ending at
12:00 midnight on
September 30, 2036
on the same terms and
conditions as in
existence for the
Initial Term.
		  	FCC Unit 2	  	Gasoline
 Light
 Cycle
Oil

Olefins
 Slurry
	  	7,600
BPD6	 	 	$13.0842/BBL8	 	 		 		  		  	$	176.25M	 	  	$	7.8M	4  	 	$	11,566	 	  		 	
		  	Polymerization
Unit	  	Gasoline
 Butane
 Propane
	  	2,438
BPD6	 	$	9.6028/BBL	8  	 		 		  		  	$	37.0M	 	  	$	3.2M	4  	 	 	—  	 	  		 	

  

	*	 As of July 1, 2018. As a result of the OPEX and CAPEX adjustments for the Applicable Assets at Woods Cross
on October 1, 2017, the Tolling Fees for the Woods Cross Applicable Assets at October 1, 2017 were readjusted as follows: Crude Unit 2: $2.6142/BBL; FCC Unit 2: $12.6614/BBL; and Polymerization Unit: $9.2925/BBL. 

	1.	 The “Feedstock” for the El Dorado Assets is light naphtha and heavy naphtha. The
“Feedstock” for the Woods Cross Assets is as follows: Crude Unit 2 – crude oil; FCC Unit 2 – crude tower bottoms and outside gas oil; Poly Unit – olefins. 

	2.	 El Dorado Only: The Tolling Fee shall never be less than $.36 per BBL of Feedstock. If as a result of a
reduction to the Tolling Fee or Minimum Throughput Commitment for a Contract Quarter pursuant to Section 2.2(d) of the Agreement, the Applicable Refinery Owner has overpaid its Tolling Fees for a Contract Quarter, the
Applicable Refinery Owner shall receive a credit against its Tolling Fees due for the following Contract Quarter in the amount of such overpayment. 

	3.	 El Dorado Only: The Tolling Fee, as previously adjusted on a cumulative basis, shall be adjusted on July 1
of each calendar year, commencing July 1, 2017, by an amount equal to a percentage calculated as follows: (A) 0.75 x the change in the PPI as described below, plus (B) 0.25 x the annual HollyFrontier Merit Compensation Adjustment (positive or
negative) for such calendar year. The change in the PPI is the upper change in the annual change rounded to four decimal places of the Producers Price Index-

  
 Exhibit C2-2 

 
Commodities-Finished Goods, (PPI), et al. (“PPI”), produced by the U.S. Department of Labor, Bureaus of Labor Statistics. The series ID is WPUFD49207– located at
http://www.bls.gov/data/. The change in PPI for each year shall be calculated as follows: annual PPI index (most current year) less annual PPI index (most current year minus 1) divided by annual PPI index (most current year minus 1); provided
that the change in PPI in any year shall not be less than one percent (1%) or more than three percent (3%). For the avoidance of doubt, if the change in PPI in any year is less than one percent (1%) (including if the change in the PPI is negative)
it will be rounded up to one percent (1%) and if the change in PPI in any year is greater than three percent (3%) it will be rounded down to three percent (3%). If either index is no longer published, the Parties shall negotiate in good faith to
agree on a new index (as applicable) that gives comparable protection against inflation or deflation, and the same method of adjustment for increases or decreases in the new index shall be used to calculate increases or decreases in the Tolling Fee.
If the Parties are unable to agree on a new index, a new index will be determined in accordance with the dispute resolution provisions set forth in the Article VIII of Omnibus Agreement, and the same method of adjustment for increases or
decreases in the new index shall be used to calculate increases or decreases in the Tolling Fee. The annual HollyFrontier Merit Compensation Adjustment is the company-wide increase (or decrease) in salary for the year in which the adjustment occurs
as determined by the HollyFrontier Chief Executive Officer and Vice President, Human Resources (excluding merit compensation adjustments for executive officers that are determined by the HollyFrontier Board of Directors (or a committee thereof) and
excluding any annual increases for union employees). Examples of the annual Tolling Fee adjustment under various scenarios are as follows: 
  

	 	(1)	 if the change in PPI is 0% and the HFC Merit Compensation Adjustment is 3.5%, the Tolling Fee adjustment would
be (0.75 x 1%) + (0.25 x 3.5%) = 1.625% 

  

	 	(2)	 if the change in PPI is 2% and the HFC Merit Compensation Adjustment is 2%, the Tolling Fee adjustment would be
(0.75 x 2%) + (0.25 x 2%) = 2% 

  

	 	(3)	 if the change in PPI is 5% and the HFC Merit Compensation Adjustment is 2%, the Tolling Fee adjustment would be
(0.75 x 3%) + (0.25 x 2%) = 2.75% 

  

	 	(4)	 if the change in PPI is 0% and the HFC Merit Compensation Adjustment is
-2%, the Tolling Fee adjustment would be (0.75 x 1%) + (0.25 x (-2%)) = 0.25% 

4. After the first turnaround on the Applicable Asset during the Applicable Term, HEP Operating will calculate its aggregate Turnaround Costs incurred in
connection therewith. In the event such aggregate Turnaround Costs for the Applicable Asset exceeds the Accrued Turnaround Cost set forth above then (A) a turnaround surcharge (the “Turnaround Surcharge”) will be added to the Tolling
Fee based on each BBL of Feedstock (using the Minimum Throughput Commitment) in order to allow HEP Operating to recover (i) such Turnaround Costs in excess of the Accrued Turnaround Cost plus (ii) a ten percent (10%) return on such excess
(the aggregate amount specified in clauses (i) and (ii), the “Turnaround Payment”). Such Turnaround Surcharge shall be paid by the Applicable Refinery Owner to HEP Operating on each BBL of Feedstock processed through the Applicable
Asset until the earlier to occur of (i) the expiration of the Applicable Term or (ii) the recovery by HEP Operating of the Turnaround Payment. In addition, the Tolling Fee will be adjusted by the amount necessary to recover the new
estimated turnaround expense for the remainder of the Applicable Term (based on the Minimum Throughput Commitment). 
 5. If at the end of any calendar month
during the Applicable Term the aggregate cost of gas incurred by HEP Operating in connection with the operation of the Applicable Assets exceeds the Assumed Fuel Gas Cost, the Applicable Refinery Owner shall promptly pay to HEP Operating an amount
equal to the positive difference, if any, of (i) the aggregate cost of fuel gas incurred by HEP Operating in connection with the operation of the Applicable Assets during such calendar month less (ii) the Assumed Fuel Gas Cost. 

6. Determined on a Contract Quarter basis. 
 7. Woods Cross Only:
The Tolling Fee, as previously adjusted on a cumulative basis, shall be adjusted on July 1 of each calendar year, commencing July 1, 2017, by an amount equal to a percentage calculated as follows: (A) 0. 5 x the change in the PPI as
described below, plus (B) 0.5 x the annual increase under the then current Woods Cross union contract. The change in the PPI is the upper change in the annual change rounded to four decimal places of the Producers Price
Index-Commodities-Finished Goods, (PPI), et al. (“PPI”), produced by the U.S. Department of Labor, Bureaus of Labor Statistics. The series ID is WPUFD49207– located at http://www.bls.gov/data/. The change in PPI for each year shall be
calculated as follows: annual PPI index (most current year) less annual PPI index (most current year minus 1) divided by annual PPI index (most current year minus 1). If either index is no longer published, the Parties shall negotiate in good faith
to agree on a new index (as applicable) that gives comparable protection against inflation or deflation, and the same method of adjustment for increases or decreases in the new index shall be used to calculate increases or decreases in the Tolling
Fee. If the Parties are 

  
 Exhibit C2-3 

 
unable to agree on a new index, a new index will be determined in accordance with the dispute resolution provisions set forth in the Article VIII of Omnibus Agreement, and the same method of
adjustment for increases or decreases in the new index shall be used to calculate increases or decreases in the Tolling Fee. The annual increase under the then current Woods Cross union contract is the annual base pay increase given to union
employees at Woods Cross, currently on or about February 1 of each year. Examples of the annual Tolling Fee adjustment under various scenarios are as follows: 

(1) if the change in PPI is 0% and the annual increase under the then current Woods Cross union contract is 3.5%, the Tolling Fee adjustment
would be (0.5 x 0%) + (0.5 x 3.5%) = 1.75% 
 (2) if the change in PPI is 2% and the annual increase under the then current Woods Cross union
contract is 2%, the Tolling Fee adjustment would be (0.5 x 2%) + (0.5 x 2%) = 2% 
 (3) if the change in PPI is 5% and the annual increase
under the then current Woods Cross union contract is 2%, the Tolling Fee adjustment would be (0.5 x 5%) + (0.5 x 2%) = 3.5%10. 
 (4) if the
change in PPI is -1% and the annual increase under the then current Woods Cross union contract is 2%, the Tolling Fee adjustment would be (0.5 x -1%) + (0.5 x 2%) =
0.5%. 
 8. Woods Cross Only: If the Applicable Refinery Owner has overpaid its monthly Tolling Fees after adjustments to Tolling Fees or Minimum Throughput
Commitments for a Contract Quarter pursuant to Section 2.2(d) of the Agreement, the Applicable Refinery Owner shall be entitled to apply any such overpayment as a credit against Tolling Fees within the succeeding twelve months for volumes of
Feedstock delivered to HEP Operating in excess of the Minimum Throughput Commitment for any of the Applicable Assets. If any such overpayment has not been credited within twelve months of the overpayment, such overpayment shall be credited against
Tolling Fees due with respect to any Minimum Throughput Commitment for any of the Applicable Assets, or if there are no such Tolling Fees due, such overpayment shall be credited against any other obligations owed by the Applicable Refinery Owner, or
its Affiliates, to HEP Operating. 
  

  
 Exhibit C2-4

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