I have a few questions about the mutant_model script. I am trying to do a single mutation modeling using this script.

optimize(s, sched)

Where S represents a group of selected atoms (Mutation position). If I understand correctly, The optimize function will do a conjugate gradient to the selected atoms to find the local energy minimum. However, after doing the minimization step, the energy function results in a small positive value which is unusual. I also tried selecting the whole structure which is about 300 residues, did the optimized step and energy computing. This time the energy function showed up with an extremely large positive value. Besides this, I tried to compute the DOPE for both nature structure and the whole sidechain refined structure and found that the DOPE for the refined model is even larger than the one for the native structure which made me so confused. 

Many Thanks,