Re: [ccp4bb] phenix target weight refinement

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Cell metric search in pdb
From: "Mark J {- dot -} van Raaij" mvrcri {- at -} IBMB {- dot -} CSIC {- dot -} ES
Date: 2010-03-13

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Subject: Re: phenix target weight refinement
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2010-03-13

Hi Salameh,
there is PHENIX bulletin board where PHENIX-specific issues are discussed:
http://www.phenix-online.org/mailman/listinfo/phenixbb
Anyway, regarding your question:
> In every refinement round the wxc and wcu are out of control,
> although I
> modify the def file and change the values of wxc=1 and wxu=1 so they
> are tightly restrained, but it failed to fix the problem, wxc and wxu
> values keep fluctuating, in my latest refinement round wxc=256!!
Without having the data (model, data and command files) I can only guess:
I presume you have a ligand with a custom CIF file that defines rediculously small
esds for torsions and which screws up the restraints target and weights.
If you send me the inputs I will have a closer look and tell what exactly is wrong.
> wxu=3.The Stereochemistry looks very loosely restrained and the
> gap between
> R-free and R-work is too big. I've been using phenix for almost 4
> yearsand never had this problem, or once I set the values of wxc
> and wxu that
> will be it, never change.
Recently we had someone with the exact same problem and my above guess was actually correct and solved the issue.
Pavel.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Cell metric search in pdb
From: "Mark J {- dot -} van Raaij" mvrcri {- at -} IBMB {- dot -} CSIC {- dot -} ES
Date: 2010-03-13

Next message:
Subject: question about MAL in monomer library
From: Minglei Zhao mlzhao {- at -} MBI {- dot -} UCLA {- dot -} EDU
Date: 2010-03-14