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*If* you are using WEIGHT AUTO, check the RMSDbonds. You don't say what your resolution is, but I assume it's in lower 2.0s. I've seen refmac5 in some cases produce somewhat unreasonable geometries (i.e. RMSDbonds>0.025A) at such medium resolution and accordingly, large R/Rfree gap. If this is the case, one suggestion is to determine the optimal weight manually (e.g. the one that minimizes Rfree). This IMLE does not lower the Rfree, but increases R, thus closing the gap. You may also consider NCS restraints if you have multiple copies. Does anyone already have the PDB-wide R/Rfree gap versus resolution data (it does not seem that the PDB maintains one)? Ed. On Mon, 2009-10-19 at 14:49 +0200, 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 > E-mail: [log in to unmask] > > > > > > This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. > --