Hi, Some of you were right, I did not try to modify weights. Previous weight was 0.03 (assigned automatically), actual is 0.01 and Rwork vs Rfree is about 0.25 and 0.33, so 8% of difference - hopefully acceptable. But now I have very low RMSDs. And then you read in this forum quite often, that we should refine against the data and not against the restraints. :)
Thanks anyway, Petr 2010/12/10 Lijun Liu <lijun....@ucsf.edu>: > Hi, > At this resolution, such a difference in Rs could be an indicator that the > structure is over--fitted. > What weight did you choose? > Lijun > On Dec 10, 2010, at 3:17 AM, Petr Kolenko wrote: > > Dear colleagues, > > I appreciate any help, or any suggestion with my difficult data. Many > thanks at least for consideration. > I work with datasets at 3.6AA of resolution. Integrated with XDS, > scaled with SCALA. After integration and scaling in P1, POINTLESS > suggested space group I432: > > Space group confidence: 0.95 > Laue group confidence: 1.000 > Total probability: 0.97 > > > After any longer refinement (more than 20 cycles), there was always a > big gap between Rwork and Rfree (0.22 and 0.33), although the > structure looks quite good at this resolution. I tried also space > group I23, here are my statistics: > > Data processing (I23 vs I432): > Rmerge - 0.124 vs 0.134 > high resolution Rmerge - 0.649 vs 0.732 > low resolution Rmerge - 0.048 vs 0.037 > > The gap between Rwork and Rfree was stabilized in I23 using tight NCS > restraints: > > Rwork vs Rfree: > I23 withouth NCS: 0.228 vs 0.334 > I23 with NCS: 0.249 vs 0.296 > I43 : 0.228 vs 0.326 > > My question is, what would you recommend me to close the gap? Or is > this Rfree pointing out a lower real symmetry (I23) than suggested by > POINTLESS or PHENIX.XTRIAGE (I432)? I have tried different selection > of free reflections in I432 dataset already, but with almost the same > results. > > Many thanks for any response. > Petr > > -- > Petr Kolenko > petr.kole...@biochemtech.uni-halle.de > http://kolda.webz.cz > > Lijun Liu > 555 Mission Bay Blvd South > CVRB Room 482, MBox 3122 > University of California, San Francisco > San Francisco, CA 94158 > Phone: (415)514-2836 > > > > -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz
