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Dear Jan, an initial increase in Rfree usually means, that either, in case of isomorphous crystal forms, the structure was refined before against a different test set, or, in case of completely different crystal forms, that you have a new test set. In both cases, Rwork and Rfree for the initial model start at very similar values and "de-couple" during refinement, resulting in decreasing Rwork and increasing Rfree values. If you have similar resolution ranges, you should define your own "standard" refinement protocol; for instance, rigid body -> TLS -> xyzB, such that the rmsd in bond lengths converge at similar values, and then compare the R-values afterwards. This can be done with all modern refinement programs, such as REFMAC, PHENIX, BUSTER and CNS. Good luck, Dirk. Am 25.02.10 15:38, schrieb Jan Schoepe: > Dear all, > > I do have a question about comparing Rfree and Rwork factors of > different refinement trials whereas I always started with the same pdb > file and structure factors (phasing by MR). > Means I had a protein structure which was (not just by me) refined > several times in different ways also with different programs and also > accordingly got different R factors for each finally refined structure. > Could anyone suggest if there is something like a "standard run" which > makes all these R factors (or "derivatives" since this run should > change the R factors) better comparable? > (E.g. it did not work for me to do a 1 cycle rigid body refinement in > refmac hoping that the R factors are measured well and the structure > does not change much. In fact, the R factors increased dramatically, > lets say Rfree from 30% to 40%.) > > Many thanks for your suggestions! > Jan > > > __________________________________________________ > Do You Yahoo!? > Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden > Schutz gegen Massenmails. > http://mail.yahoo.com -- ******************************************************* Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: [log in to unmask] WWW: www.genzentrum.lmu.de *******************************************************