[phenixbb] Phenix.Refine fix WXC has no effect

[White, Mark]

Everyone,

The problem seems to relate to using Real Space Refinement in phenix.refine, which at the final stages of refinement I usually turn off, but did not this time.  Turning off XYZ (real-space) in the GUI allows WXC to work properly.

This does seem to indicate a bug in the WXC optimization routine. Years ago I implemented an optimization scheme in CNS based on target Bond-RMSD values which can be roughly related to the number of observations / number of atoms ~ (#reflections>5sigma)/(#atoms).  The target can then be limited to physically reasonable values 0.004 < Bond-RMSD < 0.025, and you never see a bond RMSD of 0.035 Å.

Best regards,
Mark

Mark Andrew White, Ph.D.
Associate Professor of Biochemistry & Molecular Biology,
Manager, SCSB Macromolecular X-ray Laboratory
UTMB, Galveston, TX
http://xray.utmb.edu

________________________________
From: Dorothee Liebschner <dcliebschner at lbl.gov>
Sent: Monday, August 10, 2020 10:11 PM
To: Nigel Moriarty <nwmoriarty at lbl.gov>
Cc: White, Mark <mawhite at UTMB.EDU>; phenixbb at phenix-online.org <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Phenix.Refine fix WXC has no effect

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Hi Mark,

While waiting for Pavel to return, you could do the following:
Check if the rmsd goes up because all bond rmsds increase or because there are a few outrageous outliers. The validation tab after refinement lists the worst offenders for geometry restraints.

Best wishes,

Dorothee

On Mon, Aug 10, 2020 at 3:12 PM Nigel Moriarty <nwmoriarty at lbl.gov<mailto:nwmoriarty at lbl.gov>> wrote:
Mark

Pavel is best to answer this but he will return on Thursday. Someone else may offer guidance until then.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
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On Mon, Aug 10, 2020 at 1:10 PM White, Mark <mawhite at utmb.edu<mailto:mawhite at utmb.edu>> wrote:
Hello,

I am refining a 3.5 Å structure using the latest stable version of Phenix.Refine. After switching to the latest version the Bond RMSDs exploded to ~ 0.035 Å, when using optimize wxc.  Turning off Optimize and using the "Fix WXC" parameters in the GUI with increasingly smaller values had almost no effect on the final bond rmsds, which seems to explode from reasonable values in the "3_xyz" step of refinement.  Am I missing something?

Best regards,
Mark

Mark Andrew White, Ph.D.
Associate Professor of Biochemistry & Molecular Biology,
Manager, SCSB Macromolecular X-ray Laboratory
UTMB, Galveston, TX
http://xray.utmb.edu<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fxray.utmb.edu%2F&data=02%7C01%7Cmawhite%40utmb.edu%7Cd6d6cd1b274d43d4ef5d08d83da443c0%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C637327123003089881&sdata=xybNRA1dxHzyRFCmqqgWHAD4uFWDMwOzVHtQMjN3o0c%3D&reserved=0>
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