Dear ccp4 members I have something that surprises me with molecular replacement. I have obtained a solution for a single point mutation using Phaser, the solution seems ok. I do one round of refinement with refmac and I check the structure using molprobity before I even start really to refine it. The structure looks very good. MolProbity gives all green lights. Then I start to "fix" the structure, I add waters, I check fit to density, rotamers, geometry etc, I do some more refinements. I check with MolProbity and it looks a lot worse... many clashes, many bad ramachandran and rotamers, many red lights. I do not understand. How can each successive round of refinement make the structure worse and worst? Is there a fundamental problem, perhaps, like undiagnosed NCS or incorrect space group or incorrect MR solution? Could they be giving these strange result do you think?
Thanks Careina
