Optimizing Models

Dear Modellers,

It appears that I have successfully modelled a mutated protein using 'model.top' routine which generated 20 output co-ordinates to choose from. It is noted that each file contains a parameter called MODELLER OBJECTIVE FUNCTION - most possibly indicating the model quality(?). Now, the question is which value of the function to consider - the lowest one or vice versa?

Also, when I checked the secondary str. etc. of one such model using PROCHECK, several bad contacts were noted. Can you suggest any particular 'top' routine which will eventually eliminate all these / or optimize them, so as to make the model acceptable?

Thanks in advance.

Debashis