Re: [ccp4bb] an over refined structure

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008

Previous message:
Subject: Solved: PDB file column-cut-paste issues
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2008-02-07

Next message:
Subject: Re: Solved: PDB file column-cut-paste issues
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-07

Subject: Re: an over refined structure
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2008-02-07

> If you think about it, there is an analogy to relaxing geometrical
> constraints, which also allows the refinement to put atoms into
> "density". The reason it usually doesn't help Rfree is that the density
> is spurious. At least some of the incorrect structure determinations of
> the early 90's (that spurred the introduction of Rfree etc.) had high
> rms deviations, suggesting that this is how the overfitting occurred.
> Nevertheless, once hit with a bit of simulated annealing, the Rfree
> values of such models deteriorated significantly.

If memory serves, the incorrect structures of the 1990's would have had
relaxed geometry precisely because they needed to do that to reduce R,
and R used to be the primary indicator of structure quality in the days
before R-free was introduced. There's quite a big difference between
the latitude afforded by relaxing geometry and the degree of freedom
allowed by multicopy refinement. Simply increasing the RMS bond length
deviations from 0.012 to 0.035 Angstrom would move atoms on average by
only a fraction of a bond length, which is not really enough to jump
between different atom locations.

In any event, the MsbA statistics can be simply explained from an
expectation of what happens if you overfit your (wrong) structure using
techniques inappropriate for the resolution:

R-work goes down
R-free goes down less
(R-free - R-work) goes up

and this happens in general with use of multicopy refinement at anything
less than quite high resolution - I'm thinking in particular of a
comment in Chen & Chapman (2001) Biophys J vol. 8, 1466-1472. So I see
no reason to suggest NCS is having a particularly extreme, perhaps
unprecedented, effect.

Phil Jeffrey
(still working on converting Micro$loth Powerpoint to html)

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008

Previous message:
Subject: Solved: PDB file column-cut-paste issues
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2008-02-07

Next message:
Subject: Re: Solved: PDB file column-cut-paste issues
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-07