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
