Hello Everyone, I have a question about getting rid of model bias in refinement with refmac. I solved the structure with molecular replacement. After final refinement of the structure, I found out some key amino acids in the structure and wanted to make sure their conformations are correct. I omitted these amino acids (by setting occupancy to zero) and refined the structure. I manually fit the amino acids into the density and refined the structure again. I found these amino acids return to the precious conformations even though the conformations I fit were different. Should I omit these amino acids from the beginning of the refinement? What is the best way to get rid of the model bias? Your suggestions are greatly appreciated! Best, Sun
