[phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density

Pavel Afonine pafonine at lbl.gov
Thu Dec 3 09:16:16 PST 2020

Hi Igor,

please make sure to try the same refinement using the latest Phenix 
version from nightly builds first:


The latest I see here is 1.19rc7-4070.

Chances are the version you used had a bug that we fixed by now.

If the problem persists please go ahead and send me inputs and indicate 
residues that are bad and I will investigate right away!


On 12/3/20 08:42, Igor Petrik wrote:
> Thanks Nigel,
> I will put together the input and output file from my latest 
> refinement and send them to you and Pavel later today.
> - Igor Petrik, PhD
> On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund <folmerf at gmail.com 
> <mailto:folmerf at gmail.com>> wrote:
>     Dear Igor
>     There's a phenix bulletin board for question like this, which is
>     where you should post the question. ( I crosspost here)
>     I would choose to not do the real space refinement in
>     phenix.refine during the last rounds of refinement of a model,
>     when sidechain positions are essentially correct.
>     I hope this helps
>     Folmer
>     tor. 3. dec. 2020 05.48 skrev Igor Petrik <petrik1 at illinois.edu
>     <mailto:petrik1 at illinois.edu>>:
>         I am refining a 1.71A X-ray structure with phenix refine. I
>         have everything modelled in - ~150 residues in the ASU and a
>         heme - and my R-work/R-free is 0.17/0.22. But when I went to
>         deposit it, PDB pointed out that two of my sidechains have
>         distorted geometries. One is a His, and looking at it in Coot,
>         I can clearly see the 2Fo-Fc density for the correct geometry,
>         but the actual coordinates that phenix refine produce don't
>         lie in that density; there are significant difference map
>         peaks showing that the coordinates are in the wrong place. If
>         I use real space refine in Coot to put the coordinates back
>         into the correct density and refine it again in phenix, they
>         get distorted again.
>         What settings in phenix should I check to try to get it to
>         properly refine the coordinates?
>         Thanks,
>         - Igor Petrik, PhD
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