On Wed, May 29, 2013 at 5:53 AM, Benoît Masquida
I solved using MR a low resolution RNA structure taking data up to 4.3Å and a model of a structure with slight differences. However, when I try to refine, Rwork decreases quickly (start 47, final 32 but Rfree remains high (start 48, final 44). The data are pretty good up to 4.0 with I/sigma above 1. The map doesn't point clearly to wrong regions of the model. What can I try to improve the maps and build the correct model?
Standard advice at this resolution: 1. Use reference model restraints. 2. Use NCS restraints if you have NCS (at this resolution it might be worth trying both the torsion and cartesian parameterizations). 3. Optimize the X-ray/restraint weights. 4. Make lots of omit maps to ensure that you're not being deceived - model bias at this resolution really is scary. Also be careful if the outer resolution shells are incomplete, because Phenix (like Refmac) will by default fill in missing reflections with F-calc to avoid map artifacts, but this can make the model bias worse. 5. Use map sharpening - I would recommend doing this interactively in Coot rather than checking the box in Phenix. You might also want to experiment with more conservative B-factor parameterizations (grouped or TLS), although I have yet to figure out how to do this reliably (and get a better result than tightly restraint individual isotropic refinement). -Nat