[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  
- 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  
- You should look at the other validation criteria as well  
(Ramachandran, rotamers, clashscore, etc.).


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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