Thanks for the advice Pavel!

I don't want to celebrate prematurely, but I just re-ran the same refinement in both the stable and in nightly 4070, and it _seems_ to be corrected in the nightly. Will let you know if it pops up again.
On Thu, Dec 3, 2020 at 9:16 AM Pavel Afonine <pafonine@lbl.gov> wrote:
Hi Igor,

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

http://phenix-online.org/download/nightly_builds.cgi

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!

Pavel


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@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@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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