The MTA cut mega-developer Bruce Ratner a special deal on Atlantic Yards June 24, then six days later raised subway fares for everyday straphangers.

The deal - one sign these are strange economic times indeed - releases Ratner from a previous agreement to pay the MTA $100 million upfront for a nine-acre site in the Atlantic Yards development footprint known as the Vanderbilt Yards.

Instead, Forest City Ratner will pay just $20 million upfront for the site, currently a defunct Long Island Rail Road rail yard. Under the terms of the new deal, Ratner would pay off the remaining $80 million in installments ending in 2031.

Additionally, Ratner, who promised to rebuild the rail yard as part of his Atlantic Yards project, will now be required by the MTA to build a smaller, seven-track yard instead of the larger nine-track yard originally agreed upon.

The new agreement requires Ratner to complete the improved rail yard by September 1, 2016, according to an MTA staff summary of the deal.

All but two of members of the MTA board voted in favor of the deal, after listening to last-ditch appeals against it from Atlantic Yards opponents who called the agreement a "bailout" for Ratner.

"We were able to reach an agreement with the developer that we felt reflected the reality of the economic situation," said MTA spokesperson Jeremy Soffin, "while at the same time keeping in place the original value of the deal."

Soffin said the MTA's priority in negotiating a new deal was to ensure the rail yard would be rebuilt to meet transportation needs.

"From the MTA's perspective we needed to see that we're getting our needs met," said Soffin. Under the deal, he added, "our transportation needs will be met."

The deal also stipulates Ratner pay an additional $200,000 per year to have the Atlantic Avenue-Pacific Street subway station include the name Barclays Center, the name of the Nets basketball arena planned for Atlantic Yards.