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On Monday, October 25, 2010 03:16:28 pm Maia Cherney wrote: > I had a similar problem. It dissappeared when I switched the > refinement to phenix. The R factors dropped and the difference between > them became acceptable. It would be useful to pin down what the two programs did differently. It is likely that some particular default setting is the relevant quantity. - Geometric restraint weight? - B-factor restraint weight? - NCS? - hydrogen treatment? - Did you use the same set of R-free reflections in both programs? I'm currently running a bunch of parallel runs in phenix and refmac to test something else. What I notice to be the biggest difference in their default settings is that the default restraint on B factors is looser by a factor of 2-3 in phenix, whereas the default restraint on geometry is looser by a factor of ~2 in refmac. I need to adjust those for each refinement pair so that I can get comparable runs. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742