Hi Yuri,
So I am done refining a structure with around 760 residues in the model to a resolution of 2.29A. Rwork 0.18 Rfree 0.24 RMSD angle 1.1 Bond 0.008, clashscore 28.
Looks ok to me, with some room for improvement (Rfree-Rwork gap, clash-score).
As a I last round I ran optmize_weights and got some interesting numbers. Rwork 0.17 Rfree 0.23 RMSD Angle 0.68! Bond 0.003! clashscore 10.2
Looks even better! That's what weight optimization was supposed to do: http://www.phenix-online.org/newsletter/ ("Improved target weight optimization in phenix.refine") Looking at R-factors for structures in PDB that are similar to yours: Histogram of Rwork for models in PDB at resolution 2.19-2.39 A: 0.126 - 0.147 : 29 0.147 - 0.168 : 245 0.168 - 0.189 : 941 <<<< your structure 0.189 - 0.210 : 1613 0.210 - 0.232 : 1394 0.232 - 0.253 : 531 0.253 - 0.274 : 123 0.274 - 0.295 : 11 0.295 - 0.316 : 1 0.316 - 0.337 : 4 Histogram of Rfree for models in PDB at resolution 2.19-2.39 A: 0.165 - 0.188 : 31 0.188 - 0.211 : 220 0.211 - 0.235 : 848 <<<< your structure 0.235 - 0.258 : 1692 0.258 - 0.281 : 1459 0.281 - 0.304 : 522 0.304 - 0.328 : 94 0.328 - 0.351 : 19 0.351 - 0.374 : 6 0.374 - 0.397 : 1 Histogram of Rfree-Rwork for all model in PDB at resolution 2.19-2.39 A: 0.001 - 0.011 : 51 0.011 - 0.021 : 170 0.021 - 0.031 : 509 0.031 - 0.041 : 944 0.041 - 0.050 : 1238 0.050 - 0.060 : 1017 <<<< your structure 0.060 - 0.070 : 574 0.070 - 0.080 : 214 0.080 - 0.090 : 110 0.090 - 0.100 : 65 Number of structures considered: 4892 Well, looks like just average! Pavel