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the main question, which i'm surprised to see nobody has asked yet, is *how* are you "making sure, on coot, that the residues are in the allowed regions of the Ramachandran Plot" ?
At 3.35A resolution my density is no more than a tube with some features. So that, in most of the structure I cannot see, for example, a clear lobe for the peptide bond carbonyl. In those cases, rotating phi/psi a few degrees still fits my density very well. If this residue is in a disallowed Ramachandran position, then I fix it. The problem is that Refmac throws it back...
I started the refinement in CNS, and there I had not to much outliers. I always try to finish the refinement on Refmac, where I can use TLS. I thought that maybe there was a way to tell refmac to keep the configuration of those residues which appear to be as good on the allowed position as in a disallowed one.
Well, maybe I am being too picky. When I run procheck only 4.3% of the non-glycine residues are in disallowed regions of the Rama plot.
Mario Sanches
