Dear Sylvia,
The discrepancy is only 8% and that is acceptable (you may be able to
get the Rfree lower by changing the refinement program for the ultimate
rounds of refinement, or by using TLS refinement if you don't do that
already --- you don't mention what refinement program you are using).
WRT your question concerning the increase in Rfree: once you have the R
and Rfree as far down as they can be, there's only one way they can go:
back up. Also, the aim of refinement is not to minimize R and Rfree but
to get a model that matches best all available information. So checking
the values of R and Rfree is not sufficient. Is the geometry acceptable?
HTH,
Fred.
Sylvia Fanucchi wrote:
>
> 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 J
>
> **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
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