The towers had at least five sub levels you have not accounted for.

On February 26, 1993, at 12:17 p.m., a Ryder truck filled with 1,500 pounds (680 kg) of explosives, planted by Ramzi Yousef, detonated in the underground garage of the North Tower. The blast opened a 100 foot (30 m) hole through five sublevels with the greatest damage occurring on levels B1 and B2 and significant structural damage on level B3.

http://kolibri.teacherinabox.org.au/modules/en-wikipedia_for_schools-static/wp/w/World_Trade_Center.htm

The refrigeration plant on sublevel B5, which provided air conditioning to the entire World Trade Centre complex