Hi Yury, - make sure you correctly generated free-R flags, so there is no cross-talk between test/work sets. Illustration: see page number 123 here: http://cci.lbl.gov/~afonine/for_ccp4/PavelAfonine_PHENIX.pdf
- compare regular vs missing-fobs-filled maps. See pages188-190 here: http://cci.lbl.gov/~afonine/for_ccp4/PavelAfonine_PHENIX.pdf and previous discussion on phenixbb about this: http://www.phenix-online.org/pipermail/phenixbb/2009-August/002315.html Pavel. Twin refinement has yielded Rwork/Rfree values of about 0.10/0.12 > for a nice quality 1.8A dataset (Rmerge 6%, space group I4, twin fractions > 0.6/04) and almost the same R/Rfree (0.095/0.115) for another 1.5A nice > quality data set (Rmerge 6%, space group I4, twin fractions 0.74/0.26). > Refinement of untwinned data resulted in Rfree of ~32% and ~22% > respectively. REFMAC and PHENIX both have produced the same results and > almost identical R factors, which are suspiciously VERY LOW for this > resolution of data. Twin refinement in REFMAC has produced exceptional > quality maps even for 1.8A data (they look rather like 1.2A maps) - I can > not tell the same for PHENIX - maps were looking worse (may be someone has a > better idea why). > Normally twin refinement results in lowering R-factors - say, the > drop in R from 30% (without twin refinement) to 20% (with twin refinement) > would be considered normal, however we can see the drop from 32% to 12%. > I wonder if anyone else has experienced similar problems and what > would be the most reasonable explanation for that. > >
