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Yes - your real problem is probably that the Rfac is too low and that is often due to have rather loose geometry or lots of unrealistic waters in the model (RmsD on bonds of > 0.03 say..) It is all a bit unrealistic if you say your maps are good. I suspect if you tighten the geometry restraints by changing WEIGHT to a lower value, or by using WEIGHT AUTO then the Rfac will go up, the Rfree will maybe come down a little and neither the model or the maps will change in any realistic way at all! So you have shown (again) that Rfactors are not very reliable indicators of correctness! Eleanor Santarsiero, Bernard D. wrote: > I'm sure that the relative weight between your structure factors and > geometric factors is wrong. If you use the default value, 0.3, it may or > may not be too high. In CNS, the relative weight factor is calculated, but > this is not done in REFMAC. As a rough rule-of-thumb, I aim for a rmsd of > bond lengths at 0.01A and rmsd of bond angles at 1.5deg. This works > reasonably well for both CNS and REFMAC. I think you'll find that your > rmsd is quite high for the REFMAC coordinates since you've relaxed the > geometric factors too much to match the structure factor differences. > > Bernie Santarsiero > > > On Fri, March 9, 2007 8:22 pm, Nicholas Noinaj wrote: > >> Hi, >> >> I am working on a 2.4 angstrom structure that is in its final stages of >> refinement and finding that REFMAC5 is giving a large difference between R >> and Rfree (10%), 0.16 and 0.29, respectively. 2Fo-Fc maps looks great and >> there is very little density in the difference maps. My model covers the >> entire protein sequence, except for ~5 residues on N-term and 3 residues >> on C-term. I then used the model for refinement (annealing) within CNS, >> and found that R and Rfree are relatively similar, 0.2 and 0.28, but in >> better agreement. >> >> I have read other posts addressing similar questions, but still unsure >> what my problem could be, if there is one. While I don't mind repeating >> things in CNS, I would really like to learn to be completely reliable on >> CCP4 Suite as much as possible, since i really like the REFMAC5 - Coot >> duo. I would appreciate any suggestions or comments you might offer. >> Given how nice the density maps look and that the model passes procheck >> analysis with very few suggestions for further investigations, i am unsure >> when to go from here. >> >> Thanks in advance for all feedback! >> >> >> >> >> Cheers, >> Nick >> >> > > >