Hello!
Jaskolski & other experts say in "Stereochemical restraints revisited: how accurate are
refinement targets and
how much should protein structures be allowed to deviate from them?" (2007) Acta Cryst.
D63:611-620
that
quote: "A correctly set balance will be reflected in root-mean-square deviations from ideal
bond lengths in the
range 0.015-0.020 A for structures refined to R factors of 0.15-0.20."
I would set the weigth manually.
~L~
_______________________________________
Lari Lehtiö
Structural Genomics Consortium
Medical Biochemistry & Biophysics Dept.
Karolinska Institute
Stockholm, Sweden
_______________________________________
----- Original Message -----
From: Mark Mayer <[log in to unmask]>
Date: Tuesday, September 11, 2007 10:08 pm
Subject: [ccp4bb] refmac auto matrix weight - 'reasonable' rmsds
To: [log in to unmask]
> Hello all,
>
> I believer the suggested matrix weight for running refmac is
> 'auto'. I'm at the end of refinment for
> a data set that I've cut at 1.59 A, so maps are pretty. Here's the
> logfile with auto weighting ...
>
> NOTE bond rmsds !!!!!!!
>
> REMARK 3 R VALUE (WORKING SET) : .15481
> REMARK 3 FREE R VALUE : .18739
> REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4387 ; .033 ;
> .022
> REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5972 ; 2.776 ;
> 1.990
> Am I correct that at this resolution one should aim for bond rmsds
> of < 0.02. e.g for a weight of
> 1.0 the rmsd is 0.017, which seems more reasonable.
>
> REMARK 3 R VALUE (WORKING SET) : .16228
> REMARK 3 FREE R VALUE : .19032
> REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4387 ; .017 ;
> .022
> REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5972 ; 1.689 ;
> 1.990
> I know this has been discussed many times before, but expert
> opinion always appreciated.
>
> Thanks - Mark
>
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