[phenixbb] R-work is too low
Nathaniel Echols
NEchols at lbl.gov
Tue Sep 1 10:28:43 PDT 2009
On Sep 1, 2009, at 8:18 AM, Sam Stampfer wrote:
> 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
Random ideas:
- TLS (this sometimes has a huge effect on Rfree-Rwork)
- Individual ADPs (may or may not help, but appropriate to try at that
resolution)
- What are your rms(bonds) and rms(angles)? If these are very high
(or very low?) this may be the problem, and you need to optimize the
weighting.
- You should look at the other validation criteria as well
(Ramachandran, rotamers, clashscore, etc.).
-Nat
-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov
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