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

Folmer Fredslund folmerf at gmail.com
Wed Dec 2 21:46:36 PST 2020

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


tor. 3. dec. 2020 05.48 skrev Igor Petrik <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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