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The $7 billion deal that Citigroup agreed to strike with the Justice Department involves one of the largest cash penalties ever paid to settle a federal inquiry into a bank suspected of mortgage misdeeds.

But another major component of the settlement has little to do with troubled mortgages. As part of the deal, Citigroup has also agreed to provide $180 million in financing to build affordable rental housing.

The unusual arrangement, which was outlined in the deal on Monday, underscores how difficult it remains for Citigroup to shed its rocky past and how federal prosecutors are getting creative in holding the nation’s big banks accountable for losses that crippled the global financial system in 2008.

Like other settlements the government has signed with Wall Street, Citigroup’s deal requires the bank to modify mortgages of struggling homeowners. But Citigroup’s mortgage business has shrunk appreciably since the financial crisis, and the bank doesn’t service enough troubled mortgages to satisfy the monetary settlement terms for homeowner relief. So the bank agreed to finance affordable rental housing in unspecified “high cost of living areas.”

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Wall Street watchdog groups and housing advocates said the terms of the $7 billion settlement highlight how the federal government has fallen short in its effort to hold banks accountable, noting that neither Citigroup nor any of its executives have been criminally charged for the bank’s mortgage problems.

In announcing the deal on Monday, Attorney General Eric Holder said the hard-fought settlement did not absolve the bank or its employees from facing criminal charges. “The bank’s misconduct was egregious,’’ he said. “As a result of their assurances that toxic financial products were sound, Citigroup was able to expand its market share and increase profits.”

The Justice Department said Citigroup routinely ignored warnings that a significant portion of the mortgages it was packaging and selling to investors in 2006 and 2007 had underwriting defects. In one internal email cited by prosecutors, a Citigroup trader wrote, “went thru Diligence Reports and think that we should start praying … I would not be surprised if half of these loans went down.” But the bank securitized the loans anyway.

The Justice Department said it was this type of evidence that enabled prosecutors to extract a $4 billion cash penalty from Citigroup — the largest payment of its kind. That money will go into the U.S. Treasury’s general fund and is not earmarked for any particular use.

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