Dear all, I've done homology modeling of a protein. but in time of validation , procheck can't find or open the file. how can i overcome the problem? another problemm is here when i get the interactive ramchandran plot which shows several errors such as * Ramachandran plot: 96.5% core 2.3% allow 0.3% gener 1.0% disall and * Residue properties: Max.deviation: 18.0 Bad contacts: 0 * Bond len/angle: 8.2 Morris et al class: 1 1 1 G-factors Dihedrals: 0.32 Covalent: -0.06 Overall: 0.17 . is there any way to minimize these errors. Your valuable suggestion will help me a lot. Thanks in advance.
First off all Procheck is not meant for validating homology models but X-ray or NMR structures which can have unusual distribution of phi, psi angle. This does occur if you good software for homolgy modeling. Try more advanced SVM based methods like PCons, Maxcluster etc which performed well in CASP9.
In case of procheck, you can try it online by PDBSUM generate. If you have side chain clashes, try minimization or even rosetta relax procedure.