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There may be several reasons: It looks strange. Something seems to be wrong in protocols 1) Check free R flags. I have seen in few cases wrong free R. Generally number of reflections for free should be less than for work reflections 2) Check TLS refinement. You may need to restart TLS refinement. At this resolution I would try anisotropic refinement. If your output pdb file has aniso card then it may be the resason. Refmac by default uses isotropic refineemnt and removes all aniso cards. You can turn on aniso refinement 3) Check hydrogens. Adding hydrogens in their riding position may make difference 4) Check twin refinement 5) Anisotropic refinement If above reasons are not applicable to your case then you can send the data and I can check what is wrong. regards Garib On 13 Jul 2010, at 20:32, Ariel Talavera wrote: > Hi CCP4ers, > > Is there any differences in the way of calculating the Rfactor between > PHENIX.refine and other programs implemented in CCP4i, like Refmac5 or > sfcheck, or the EDS server? > > I asking this because I have a structure solved at 1.4 Å resolution. > Phenix,refine was used for its refinement and for the final model > Rfactor was 14.5%. But during the validation with sfcheck (CCP4i), I > got > an Rfactor of 20.8%. The same happened when I used this final model as > starting model for a refinement with Refmac5. Again I got an Rfactor > of > 20.8%. > > As far as I know, Phenix uses different algorithms for the refinement > than other programs, which in some cases can make Phenix gets better > Rfactors. Could these differences be the reason for this large > difference in the calculated Rfactors? Or I have to recheck my > procedure > for mistakes? > > Thanks a lot in advanced. > Looking forward to hearing form you. > > Cheers, > Ariel