Hi Sivia, you say the resolution is 1.8A, and your R-work=0.19 and R-free=0.27. Here is the distribution of R-factors for structures in PDB deposited at similar resolution (in range between 1.75A and 1.85A): Histogram of Rwork for all model in PDB at resolution 1.75-1.85: 0.114 - 0.130 : 6 0.130 - 0.147 : 48 0.147 - 0.163 : 221 0.163 - 0.180 : 484 0.180 - 0.196 : 718 <<< your structure 0.196 - 0.212 : 508 0.212 - 0.229 : 271 0.229 - 0.245 : 105 0.245 - 0.262 : 20 0.262 - 0.278 : 7 Histogram of Rfree for all model in PDB at resolution 1.75-1.85: 0.153 - 0.171 : 17 0.171 - 0.190 : 127 0.190 - 0.208 : 380 0.208 - 0.227 : 647 0.227 - 0.245 : 648 0.245 - 0.263 : 360 0.263 - 0.282 : 132 <<< your structure 0.282 - 0.300 : 64 0.300 - 0.319 : 10 0.319 - 0.337 : 3 Histogram of Rfree-Rwork for all model in PDB at resolution 1.75-1.85: 0.001 - 0.013 : 41 0.013 - 0.025 : 336 0.025 - 0.036 : 852 0.036 - 0.048 : 693 0.048 - 0.060 : 309 0.060 - 0.072 : 98 0.072 - 0.084 : 40 <<< your structure 0.084 - 0.095 : 11 0.095 - 0.107 : 4 0.107 - 0.119 : 4 You also mentioned you cut the data off (the actual resolution is 1.6A). Doing so just to improve R-factor doesn't seem like a good idea. Similar histograms for structures at around 1.6A resolution: Histogram of Rwork for all model in PDB at resolution 1.55-1.65: 0.099 - 0.119 : 5 0.119 - 0.138 : 26 0.138 - 0.158 : 132 0.158 - 0.177 : 349 0.177 - 0.197 : 447 <<< your structure 0.197 - 0.217 : 281 0.217 - 0.236 : 129 0.236 - 0.256 : 17 0.256 - 0.275 : 6 0.275 - 0.295 : 1 Histogram of Rfree for all model in PDB at resolution 1.55-1.65: 0.137 - 0.156 : 6 0.156 - 0.175 : 45 0.175 - 0.195 : 208 0.195 - 0.214 : 391 0.214 - 0.233 : 395 0.233 - 0.253 : 200 0.253 - 0.272 : 96 <<< your structure 0.272 - 0.291 : 37 0.291 - 0.311 : 12 0.311 - 0.330 : 3 Histogram of Rfree-Rwork for all model in PDB at resolution 1.55-1.65: 0.001 - 0.010 : 27 0.010 - 0.019 : 217 0.019 - 0.029 : 374 0.029 - 0.038 : 350 0.038 - 0.047 : 233 0.047 - 0.056 : 106 0.056 - 0.065 : 49 0.065 - 0.075 : 23 0.075 - 0.084 : 10 <<< your structure 0.084 - 0.093 : 4 Pavel. On 10/19/09 5:49 AM, Sylvia Fanucchi wrote: > > Dear all > > I have been refining my structure using refmac5 restrained refinement > and the model currently has an R-factor of 0.19. What is concerning me > is that there is quite a big discrepancy between the Rfree and the > R-factor, with the Rfree being around 0.27. Furthermore, after about > 10 rounds of refinement, the R-free actually starts to increase > slightly although the R-factor continues to decrease. Does this mean > that there is significant bias in my model? Does anybody know how I > could go about addressing this problem? > > Thanks for any help J > > **Sylvia Fanucchi Ph.D** > > **Protein Structure-Function Research Unit** > East Campus, Gate House Room 416 > School of Molecular and Cell Biology > University of the Witwatersrand > Johannesburg 2050 > South Africa > > Tel: +27 (11) 717-6348 Fax: +27 (11) 717-6351 > E-mail: [log in to unmask] <mailto:[log in to unmask]> > > > > This communication is intended for the addressee only. It is > confidential. If you have received this communication in error, please > notify us immediately and destroy the original message. You may not > copy or disseminate this communication without the permission of the > University. Only authorized signatories are competent to enter into > agreements on behalf of the University and recipients are thus advised > that the content of this message may not be legally binding on the > University and may contain the personal views and opinions of the > author, which are not necessarily the views and opinions of The > University of the Witwatersrand, Johannesburg. All agreements between > the University and outsiders are subject to South African Law unless > the University agrees in writing to the contrary. >