Re: [ccp4bb] an over refined structure

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Subject: Re: Question about strange MR solution
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-02-05

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From: "Carpenter, EP (Liz)" liz {- dot -} carpenter {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2008-02-05

Subject: Re: an over refined structure
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-02-05

I agree that the difference in Rwork to Rfree is quite acceptable at
your resolution. You cannot/ should not use Rfactors as a criteria for
structure correctness.
As Ian points out - choosing a different Rfree set of reflections can
change Rfree a good deal.
certain NCS operators can relate reflections exactly making it hard to
get a truly independent Free R set, and there are other reasons to make
it a blunt edged tool.

The map is the best validator - are there blobs still not fitted? (maybe
side chains you have placed wrongly..) Are there many positive or
negative peaks in the difference map? How well does the NCS match the 2
molecules?

etc etc.
Eleanor

George M. Sheldrick wrote:
> Dear Sun,
>
> If we take Ian's formula for the ratio of R(free) to R(work) from his
> paper Acta D56 (2000) 442-450 and make some reasonable approximations,
> we can reformulate it as:
>
> R(free)/R(work) = sqrt[(1+Q)/(1-Q)] with Q = 0.025pd^3(1-s)
>
> where s is the fractional solvent content, d is the resolution, p is
> the effective number of parameters refined per atom after allowing for
> the restraints applied, d^3 means d cubed and sqrt means square root.
>
> The difficult number to estimate is p. It would be 4 for an isotropic
> refinement without any restraints. I guess that p=1.5 might be an
> appropriate value for a typical protein refinement (giving an R-factor
> ratio of about 1.4 for s=0.6 and d=2.8). In that case, your R-factor
> ratio of 0.277/0.215 = 1.29 is well within the allowed range!
>
> However it should be added that this formula is almost a
> self-fulfilling prophesy. If we relax the geometric restraints we
> increase p, which then leads to a larger 'allowed' R-factor ratio!
>
> Best wishes, George
>
>
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-2582
>
>
>

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CCP4bb <-- 2008 <-- February 2008 <-- 05 February 2008

Previous message:
Subject: Re: Question about strange MR solution
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-02-05