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@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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