Hi Sylvia
You didn't make it clear on what basis you think the discrepancy between
R and Rfree is too big, since the Rfree you would expect to get if the
refinement were bias-free depends a lot on a number of factors such as
the resolution, the data completeness, what parameters you are refining,
what restraints you are using, whether the restraint weights are
optimal, the solvent content etc. So to judge whether Rfree is indeed
higher than would be expected I would need to know a lot more about the
refinement. Otherwise it's a bit like asking "how long does a piece of
string have to be?" - I would need to know the purpose of the piece of
string!
Also Rfree is only meaningful at convergence at refinement (you may as
well ignore all other printed values - they are worthless!). So it's
not meaningful to compare Rfree during a refinement with the final value
at convergence. It's only meaningful to compare Rfree values obtained
at convergence of refinements done under different conditions, for
example, different parameterisation, different weights, different no of
waters (provided only that you don't use different X-ray data or
restraints).
Cheers
-- Ian
> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of Sylvia Fanucchi
> Sent: 19 October 2009 13:49
> To: [log in to unmask]
> Subject: how to improve Rfree?
>
>
>
> Dear all
>
> I have been refining my structure using refmac5 restrained refinement
and
> the model currently has an R-factor of 0.19. What is concerning me is
that
> there is quite a big discrepancy between the Rfree and the R-factor,
with
> the Rfree being around 0.27. Furthermore, after about 10 rounds of
> refinement, the R-free actually starts to increase slightly although
the
> R-factor continues to decrease. Does this mean that there is
significant
> bias in my model? Does anybody know how I could go about addressing
this
> problem?
>
> Thanks for any help :-)
>
> Sylvia Fanucchi Ph.D
>
> Protein Structure-Function Research Unit
> East Campus, Gate House Room 416
> School of Molecular and Cell Biology
> University of the Witwatersrand
> Johannesburg 2050
> South Africa
>
> Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351
> E-mail: [log in to unmask] <mailto:[log in to unmask]>
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