My usual targets are 0.010 for the bonds and 1.50 for the angles.
Bernie Santarsiero
On Tue, September 11, 2007 3:22 pm, Lari Lehtio wrote:
> 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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