You havent got an incorrect CISPEP definition lurking in the PDB file
have you - COOT does NOT correct these so if you rebuild something which
has been previously flagges as CISPEP ( and that can happen if a very
ugly omega angle falls to 89.999 ) then it stays that way in the PDB
output from COOT, and REFMAC struggles valiantly to reconstruct a CISPEP..
Eleanor
Jan Abendroth wrote:
> 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
>
>
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