Josmar R. da Rocha wrote: ... > The model is built normally. However, I noticed that many residues in > the active site (which is localized in the interface between each pair > of monomers) that are supposed to exposed are turned inside out.

This is probably because your starting structure contains steric clashes between the sidechains in the interface region, and the easiest way the optimizer found to minimize these clashes was to bury the sidechains. You could try building multiple models - each model will have a different starting structure and so chances are that at least some of them will not have this problem. Or you could take the .ini file (starting structure) from your first run, and modify it manually (perhaps with something like PyMol's sculpting) to put your interface residues in a sensible position, to guide the optimizer towards the desired solution. Or you could add some restraints to those sidechains to keep them exposed - perhaps upper bound distance restraints between Cbetas in the two chains.

Ben Webb, Modeller Caretaker