Today is the deadline set 90 days ago by Governor Pataki for negotiations to end between the Port Authority, which owns the World Trade Center site, and developer Larry Silverstein, and the consensus among several real estate analysts is that some kind of deal could be reached this week mandating a considerably different configuration of building rights on the site.

Talks between Mr. Silverstein, the Port Authority, and representatives of the governor proceeded late into the night yesterday in hopes that a deal would be reached soon. The chairman of the Port Authority, Anthony Coscia, has said that the agency is seeking to take over part of the site from Mr. Silverstein, a position supported by the Bloomberg administration. Last week, representatives of Silverstein Properties, which holds a 99-year lease on the World Trade Center site, maintained that the developer has the ability and the legal rights to build out the entire site.

Yesterday, at the request of the president of Manhattan, Scott Stringer, the city’s Independent Budget Office released a report on the demand for new office space as it relates to plans for rebuilding ground zero.

Mr. Silverstein and the Bloomberg administration have produced conflicting estimates on how much rent the nearly 10 million square feet of office space planned for the World Trade Center site will command. The city says the expected rents are too low, making the project impossible to finance and creating the likely scenario that Mr. Silverstein will default in four or five years and leave part of the site unbuilt.

The IBO’s report expresses optimism that office rents will rise in Lower Manhattan, in particular because of plans for improved transportation infrastructure and an increasing presence of residential and retail properties. The report does warn, though, that both the city’s and Mr. Silverstein’s rent estimates for commercial space are too high.

“It’s a mixed bag,” a spokesman for the IBO, Douglas Turetsky, said. “There is a need for more office space. On the other hand, its unclear that rents will be sufficient for the World Trade Center development to be built out as currently planned.”

The Bloomberg administration, through a spokeswoman, seized on the report as more evidence that the lease between Mr. Silverstein and the Port Authority should be dramatically changed. The city is holding back $1.67 billion in tax-exempt Liberty Bonds to provoke a renegotiation of the lease.

The World Trade Center project director for Silverstein Properties, John Lieber, said the report underestimated future rents. “We believe the IBO made a mistake when it cited a single, across the-board rental average for downtown space as the relevant benchmark. The market for 73-year-old buildings is totally different than for brand-new office towers, which will command a substantial premium,” Mr. Lieber said.

Early yesterday morning, about a dozen construction workers began site preparation for the World Trade Center memorial. The first signs of activity were met with protests by relatives of those who lost their lives on September 11, 2001.

Several victims’ relatives have vowed to sleep next to the construction site until the plans are changed, and a group of victim’s family members, the Coalition of 9/11 Families, filed a lawsuit on Friday aimed at halting construction of the memorial to preserve the historic footprints of the twin towers.

A spokesman for the Lower Manhattan Development Corporation, John Gallagher, called the lawsuit “obstructionist” and said construction would continue as planned. The project, which could cost up to $1 billion, according to Mayor Bloomberg, is scheduled to be completed by 2009.

As negotiations on a settlement regarding the plan for ground zero continue, reports have emerged from several sources that there are internal disagreements within the Port Authority, a bistate agency with appointees from both New York and New Jersey.

A former executive director of the Port Authority, George Marlin, a Pataki appointee, said the $6 billion Trans-Hudson Express tunnel, which would add a new tunnel under the Hudson River and double New Jersey Transit’s capacity into Midtown Manhattan, could figure into negotiations.

Mr. Marlin said it’s “shakedown time” for the Port Authority, and that the tunnel project could be the “pound of flesh” that the New Jersey faction is seeking to extract from a deal at ground zero.