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 mailto:[email protected]> 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 mailto:[email protected]>:

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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Hi Michal, thanks for the info! Yes, there was a bug at some point that we fixed right after we discovered it. So it's best to use the latest version from nightly builds. Pavel On 12/3/20 09:19, Boniecki, Michal wrote:

I had similar case with Tyr side chain, but after installing latest upgrades worked fine

Michal

On 12/3/20 11:16 AM, Pavel Afonine wrote:

...

CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to [email protected]

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 mailto:[email protected]> 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 mailto:[email protected]>:

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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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 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 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 :

...

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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