Thomas Jefferson School of Law, plagued with costs associated with its new $90 million building, has reached a restructuring agreement that cuts its debt by nearly $87 million.

The deal involves nearly 90 percent of its bondholders, who will become owners of the school’s San Diego building, which opened in 2011. The school, which will lease the building, will cancel bonds and cut in half its $12 million in annual cash flow obligations in the form of quarterly payments on the debt’s principal and interest. Under the deal, reached on Tuesday, the school will pay $5 million in rent plus $1 million in interest each year.