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

[Igor Petrik]

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 at 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 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>:
>>
>>> 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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