[modeller_usage] Residues in disallowed region

Hello, Modeller:

The models built from Modeller 8v1 contain some residues (non-Gly and non-Pro) in the disallowed region based on Ramachandran plot. I wonder how this could happen? How to change these residues back to allowed region?

I try to use energy minimization such as NAMD and Amber. After all, the minimized models had increased numbers of residues in the disallowed region.

Thank you for your advice

Bo