Hi all, along the lines of a recent discussion: At the final stages of the refinement of a structure which a whole bunch of ncs (2x4chains) at 2.2A resolution in P1, I run into the following very annoying and persistent problem. The Ramachandran plot shows a whole bunch of ugly outliers. While some of them appear to be "true", ie. the same outliers in all chains w/o application of ncs, loop region, H-bonds that make sense, ..., there are a number of "misbehaving" outliers: After reciprocal space refinement some residues violate the Ramachandran plot for one or two chains only. Both 2FoFc and FoFc density clearly show that the main chain is supposed to be at a slightly different position. Real space refinement in coot puts the mainchain nicely in place on top of the ncs mates' position. Refmac then pulls things back into the forbidden region. For an illustration see here: http://picasaweb.google.com/Jan.Abendroth/RefmacAndRamachandran/
I have tried to tie down the violators with tight ncs restrains - no success. I am running refmac 5.3.0037, with TLS refinement. Rfactors seem really decent (20%/25%) as does geometry. Refmac complains about "MAKE_U_POSITIVE" problems. Any ideas? Cheers Jan -- Jan Abendroth deCode Biostructures Seattle/Bainbridge Island, WA, USA work: [EMAIL PROTECTED] home: [EMAIL PROTECTED]
