A round of refinement with simulated annealing followed by minimization should address your concern. Pavel
On Wed, Oct 11, 2017 at 4:48 PM, Karsten Dreifus <[email protected]> wrote: > Dear all, > I have a 120 aa protein. Matthews coefficient indicates 3 mol in asu. > Molrep (template with 70 % seq identity) finds three NCS molecules > (the template model has only 1 chain as it is in different space > group). Now, REFMAC refines it to 25/30 % R/RFREE. I was just worried > about model bias, so I just deleted chain C and re-ran the refinement. > I observe that in the place of chain C, the DELFWT map in Coot shows > negative density (red colour). Shouldnt the deleted regions show > POSITIVE density (green colour)? The 2fo-fc map in the deleted region > shows usual blue colour. I shook the 2chain model with Phenix simple > dynamics and then ran refinement with same results. > > How do I verify the model is correct? > Karsten >
