I'm having a problem producing a good idealized PDB file for a monomer with about 700 residues. The resulting idealized structures have positive scores that are two orders of magnitude larger than the wildtype and they look somewhat unraveled.
Is the number of residues a factor in causing these problems?
I also noticed that the wildtype protein had positive score above 800. Does this indicate that I should minimize the starting pdb structure before I idealize it or is that not a factor?