Negotiations over the terms of a $2.5 billion development agreement for two new seismically safe hospitals in The City remained in a stalemate Monday, with California Pacific Medical Center officials refusing to modify a part of the deal that Mayor Ed Lee now has concerns about. While the centerpiece of the deal is a new 555-bed hospital on Cathedral Hill, at issue is the long-term future of St. Luke’s Hospital, which serves primarily lower-income patients in the Mission district and surrounding areas.