Hi Paul,

I have been seeing this occasionally with coot 0.8.4 onward (currently using 
0.8.7-pre) even with data to 2.5 Å.  It usually happens if I use the “auto fit 
rotamer" on a neighbouring residue.
It can be tricky to sort out sometimes taking several goes with “regularise 
zone” then “real space refine”.



Martin G Montgomery
ATP Synthase Group
MRC Mitochondrial Biology Unit
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road 
Great Britain


> On 13 Oct 2016, at 02:45, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:
> On 12/10/2016 13:43, Kevin Jude wrote:
>> I am frequently getting distortions of proline residues during real space 
>> refinement -
>> specifically, close approaches between C and CD (pictured). It's hard to 
>> nail down exactly
>> what is happening but it seems like planar peptide restraints aren't working 
>> for Pro
>> residues.
> That's weird - I have not seen that before. The C-N-CD angle restraints 
> should keep these atoms apart.  You should tabulate ligand distortions to 
> investigate.
> Paul.

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