Hi Careina,
Assuming you don't suffer from a very poor data parameter ratio that would lead to such a large R-free/R, you need to improve your refinement. If you have NCS you should use local NCS restraints. You could also try jelly-body restraints, although they may not work at your resolution.
Cheers,
Robbie
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> Date: Wed, 13 Jul 2011 08:38:38 -0700
> From: [log in to unmask]
> Subject: [ccp4bb] large R-Rfree difference in "final" structure
> To: [log in to unmask]
>
> Dear ccp4 bulletin board
>
> I just have a slight concern regarding my Rwork Rfree difference. I
> have a structure that I have solved. I am reasonably content that it is
> complete because it has refined well, it no longer has bad geometries
> and contacts and all the rotamers, ramachandra, bond lengths etc are
> good. It gives favourable scores on molprobity and procheck. My only
> concern is the R factor difference. The resolution of the structure is
> 2.3A. The R factor is 0.24 after refinement but the Rfree is 0.33 which
> seems to me to be rather high. Should I be concerned?
>
> During refinement Rfree only drops from about 0.36 to 0.33 while the R
> factor drops from 0.31 to 0.24.. I have removed automatic weighting in
> refmac in order to constrain my bond lengths and angles during a couple
> of rounds of refinement. This did not have any effect on the R factors,
> however. I am fairly content that the space group I have chosen is
> correct so I am not sure what else could cause the big difference in R
> factors? There is no twinning.
>
> Can I be satisfied that my structure is correct despite the high R free
> or should I be doing other checks/ trying other things before I can
> submit this structure?
>
> Thank you for any help
> Careina
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