Adjusted EBITDA for the period was $647 million, an increase of $162 million compared to the second quarter 2018. This increase was principally driven by strong gasoline and diesel margins across our company, along with our first full-quarter contribution from Sonneborn. The Refining and Marketing segment reported adjusted EBITDA of $556 million, compared to $385 million for the second quarter of 2018. Strong product margins in all of our regions resulted in a consolidated refinery gross margin of $19.64 per produced barrel, a 19% increase, compared to the $16.57 for the same period last year.

Our Lubricants and Specialty Products business reported adjusted EBITDA of $29 million despite weakness in the base oil market. Rack Forward adjusted EBITDA was $64 million for the quarter, and adjusted EBITDA margin was 13% of sales. The strength in Rack Forward earnings was driven by improved finished product margins. Our integration of Sonneborn is progressing well, and as of July 30, we have achieved run-rate synergies of $9 million and continue to expect long-term synergies of $20 million per year.

Holly Energy Partners reported EBITDA of $89 million for the second quarter, compared to $82 million in the second quarter of last year. Higher crude oil pipeline volumes around the Permian Basin and our crude pipeline systems in Wyoming and Utah contributed to a 10% increase in volumes year over year. During the quarter, we returned $246 million of cash to shareholders through our regular dividends and share repurchases. Looking forward, we will continue our focus on improving reliability across our refining system and successfully integrating Sonneborn, further strengthening our earnings profile.

With no major planned downtime until September, our refineries are well-positioned for strong operational and financial performance in the third quarter. I'll now turn the call over to Jim for an update on our operations.

Jim Stump -- Senior Vice President, Refining

Thank you, George. For the first quarter, our crude throughput was 453,000 barrels per day, within our guidance of 445,000 to 455,000 barrels per day. Crude throughput was impacted by the two-week precautionary shutdown at our Tulsa Refinery due to flooding in the Tulsa area. Our consolidated operating cost of $5.73 per throughput barrel was $0.16 lower versus last year.

In the Mid-Con, we ran 264,000 barrels per day of crude. Opex per throughput barrel was $4.92 and was elevated versus the same period last year due to the two-week outage in late May and early June at Tulsa. Our El Dorado Refinery set a quarterly crude charge rate in the second quarter averaging 158,000 barrels per day. In the Southwest, we ran 109,000 barrels per day of crude and improved our operating expense per throughput barrel to $4.63 versus the $5.25 we recorded in the second quarter of 2018.

In the Rockies, we ran 80,000 barrels per day of crude. Our opex expense was $9.84 per throughput barrel, a 26% decrease over the same period last year. We have planned maintenance at Navajo and a planned turnaround that Cheyenne, both scheduled to begin in September. And we expect to run between 440,000 and 450,000 barrels per day of crude in the third quarter.

I will now turn the call over to Tom for an update on our commercial operations.

Tom Creery -- President, Refining and Marketing

Thanks, Jim, and good morning, everyone. As Jim previously mentioned, in the second quarter of 2019, we ran 453,000 barrels a day of crude oil. This was composed of 35% Permian and 20% WCS and black wax crude oil. Our average laid-in crude cost was under WTI by $3.35 in the Rockies, $0.25 in the Mid-Con and $0.94 in the Southwest.

In the second quarter of 2019, gasoline inventories in the Magellan system started the quarter at 7.7 million barrels and ended the quarter at 6.9 million barrels. Current inventories of Group III gasoline remain relatively static at 6.7 million barrels. This is in keeping with the five-year average volume. Group III diesel inventories rose by 1.1 million barrels throughout the period to finish at 8.1 million barrels.

Second quarter 3-2-1 cracks in the Mid-Con were $19.99, $31.30 in the Southwest and $32.19 in the Rockies. In our Southwest and Rocky regions, we saw higher margins as refinery operation issues on the West Coast affected markets in both Phoenix and Las Vegas. Crude differentials compressed across the heavy and sour slates during the second quarter. In the Canadian heavy market, second-quarter crude differentials for WCS at Hardisty averaged $11.13, slightly below first-quarter levels.

Apportionment on the Enbridge system remained high at 40% despite the continuation of production cutbacks by the Alberta government. The forward market for WCS remains wider as the market foresees incremental crude production, coupled with perceived positive impact from IMO 2020. We continue to be able to purchase and deliver adequate volumes of price-advantaged heavy crude oil from Canada to meet our refining needs. Canadian heavy and sour runs averaged 76,000 barrels a day at our plants in the Mid-Con and Rocky regions.

We refined approximately 160,000 barrels per day of Permian crude in our refining system composed of 100,000 barrels per day at the Navajo complex and 60,000 barrels per day delivered by the Centurion pipeline to our refinery at El Dorado. Midland differentials averaged the quarter at $2.13 under WTI. And currently, we see the same differential trading at around $0.70 below Cushing as new pipeline capacity is expected to come onstream. We anticipate for the remainder of this year the differential to narrow as additional pipeline comes on.

Our rent expense for the quarter was $31 million, a $25 million degrees versus the $56 million in the same period last year. And with that, let me turn the call over to Rich.

Rich Voliva -- Executive Vice President and Chief Financial Officer

Thank you, Tom. As George mentioned, the second quarter included a few unusual items. Pretax earnings were negatively impacted by a goodwill impairment of $153 million, a lower cost or market charge of $48 million and Sonneborn integration costs of $4 million. The table of these items can be found in our press release.

For the second quarter, cash flow from operations was $753 million, including turnaround spending of $31 million. HollyFrontier's stand-alone capital expenditures totaled $50 million in the quarter, producing free cash flow of $696 million. The second-quarter free -- strong free cash flow allowed us to return a total of $246 million of cash to shareholder, comprised of a $0.33 per share regular dividend totaling $57 million, as well as the repurchase of approximately 4.5 million shares of common stock totaling $189 million. And as of June 30, we had approximately $509 million remaining on our share repurchase authorization.

Over the past 12 months, we're continuing to invest across our three business. HollyFrontier has returned over $800 million of cash to shareholders through both dividends and share repurchase, representing a cash yield of 10%. At the end of the second quarter, our total cash balance stood at $915 million, which is above our targeted cash balance of $500 million. This strong cash position, along with our undrawn $1.35 billion credit facility, puts our total liquidity at over $2.3 billion.

As of quarter end, we had $1 billion of stand-alone debt and a debt-to-capital ratio of 14%. Total HEP distributions received by HFC in the second quarter were $37 million, a 2% increase over the same period in 2018. HollyFrontier owns 59.6 million HEP limited partner units, representing 57% of HEP's LP units with a market value of $1.7 billion as of last night's close. A few guidance items for 2019.

We continue to expect to spend between $470 million and $510 million for both stand-alone capital and turnarounds in our Refining and Marketing business, $40 million to $50 million at HollyFrontier Lubes and Specialties and $30 million to $40 million of capital at HEP. We anticipate an elevated cash balance through the third quarter ahead of planned maintenance at both our El Dorado and Cheyenne refineries into the fourth quarter. In our Lubes and Specialty Products business, due to both the continuing sales impacts on the flooding-related shutdown at our Tulsa facility, as well as previously unplanned maintenance at Tulsa lube extraction unit in October, we're revising our annual Rack Forward guidance to $240 million to $260 million. We continue to expect $25 million to $30 million of Sonneborn integrate costs, implying another $9 million to $14 million, which will stretch into 2020.

In the second quarter, due to the goodwill asset impairment, our effective tax rate was slightly elevated to 29%. Based on this, we now expect our full-year effective tax rate to land at 25% to 27% and to revert back to normalized levels of 24% to 26% in 2020. And with that, Stacy, we're ready to take questions.

Questions & Answers:

Operator

[Operator instructions] Thank you. I will now turn the call back over to Craig.

Craig Biery -- Director, Investor Relations

Thanks, everyone. We appreciate you taking the time to join us on today's call. If you have any follow-up questions, as always, reach out to investor relations. Otherwise, we look forward to sharing our third-quarter results with you in October.

Operator

[Operator signoff]

Duration: 16 minutes

Call participants:

Craig Biery -- Director, Investor Relations

George Damiris -- President and Chief Executive Officer

Jim Stump -- Senior Vice President, Refining

Tom Creery -- President, Refining and Marketing

Rich Voliva -- Executive Vice President and Chief Financial Officer

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