After modeling a protein using modeller some residues remain in the
disallowed regions of ramachandran plot. Is that model incorrect ? Is
there any way to remove bad contacts and residues in disallowed regions
after modeling? I tried to overcome this problem using Deepview by
selecting two or more residues and building loop. Though the residues in
disallowed regions and bad contacts become zero by this procedure but
structure is affected. What should I do please guide me.
Yes, you will occasionally find some residues in disallowed regions. If
it really bothers you, you should build multiple models and pick the
best one.