My experience is also that the bulk solvent model sometimes makes the mask exclude internal large cavities.
Laurie Betts On Fri, Apr 12, 2013 at 12:03 PM, Pavel Afonine <pafon...@gmail.com> wrote: > P.S.: you are not alone having such R-factors > > On Fri, Apr 12, 2013 at 9:50 AM, Jan van Agthoven <janc...@gmail.com>wrote: >> >>> Could this be due to an excessive low R >>> factor that phenix.refine has generated: R=17.9 and Rfree=23.3 at a >>> resolution of 2.85 A? >> >> > Histogram of Rwork for models in PDB at resolution 2.75-2.95 A: > 0.134 - 0.157 : 10 > 0.157 - 0.180 : 75 <<<<< your model > 0.180 - 0.203 : 365 > 0.203 - 0.226 : 666 > 0.226 - 0.249 : 653 > 0.249 - 0.272 : 247 > 0.272 - 0.295 : 52 > 0.295 - 0.318 : 11 > 0.318 - 0.341 : 1 > 0.341 - 0.364 : 1 > Histogram of Rfree for models in PDB at resolution 2.75-2.95 A: > 0.191 - 0.210 : 27 > 0.210 - 0.230 : 105 > 0.230 - 0.249 : 271 <<<<< your model > 0.249 - 0.269 : 472 > 0.269 - 0.288 : 649 > 0.288 - 0.308 : 377 > 0.308 - 0.328 : 129 > 0.328 - 0.347 : 34 > 0.347 - 0.366 : 14 > 0.366 - 0.386 : 3 > Histogram of Rfree-Rwork for all model in PDB at resolution 2.75-2.95 A: > 0.001 - 0.011 : 23 > 0.011 - 0.021 : 87 > 0.021 - 0.030 : 195 > 0.030 - 0.040 : 377 > 0.040 - 0.050 : 407 > 0.050 - 0.060 : 408 <<<<< your model > 0.060 - 0.070 : 296 > 0.070 - 0.079 : 162 > 0.079 - 0.089 : 81 > 0.089 - 0.099 : 45 > Number of structures considered: 2081 > > The above histograms were obtained using command: > > phenix.r_factor_statistics 2.85 > > Pavel > >
