Dibyabhaba Pradhan wrote: > I modelled number of proteins by basic modelling. After basic > modelling during procheck evaluation the residues in most favorable > region is generally above 90% but after loop refinement the residues > in most favorable region comes below 90%. Please kindly inform me what > may be the region for this. > > Also after energy minimization the the percentage of residue in most > favorable region decreses.
I'm not sure what this has to do with phosphorylation, but there is certainly no guarantee that a single minimization will give a "better" model. You'd be better off building several models to get a reasonable sampling of the energy landscape and then picking the best cluster or single model.
Ben Webb, Modeller Caretaker