Hi,
I'm refining a 2.88
Angstrom structure and am getting a difference of greater than 6%
between the R-work and R-free. The best result (I think) is what I
have from minimization alone:
Start R-work =
0.3219, R-free = 0.3505 (no bulk solvent and anisotropic scale)
Final R-work =
0.2424, R-free = 0.3174 (no bulk solvent and anisotropic scale)
Start R-work =
0.3220, R-free = 0.3500
Final R-work =
0.2411, R-free = 0.3176
The results from simulated annealing are the following:
Start R-work = 0.3219, R-free = 0.3505
(no bulk solvent and anisotropic scale)
Final R-work = 0.2454, R-free = 0.3322
(no bulk solvent and anisotropic scale)
Start R-work = 0.3220, R-free = 0.3500
Final R-work = 0.2403, R-free = 0.3333
I have also done the refinement with ncs but ncs is probably not appropriate for my structure. The final R-free ends up being higher (though the difference between R-free and R-work ends up being 6-7%)
My PI (who is on vacation until next week) said that it was a
problem if R-work was more than 0.06 lower than R-free. Any
recommendations for me? Is it possible to reduce this difference? Is it worth it to rebuild the refined pdb if the R-work is this different from the R-free?
My refinement script is:
phenix.refine ss46_p3_cv.mtz ss46_rebuilt.pdb \
output.prefix=results/ss46_rebuilt_sa \
strategy=individual_sites+group_adp cif_link.params nag-nag.cif \
twin_law="h,-h-k,-l" \
simulated_annealing=true
(the cif_link.params and nag-nag.cif files are made to handle the N-glycosylation sites, I think).
Thanks for your help!
-Sam