[phenixbb] R/ R free (overall) and R/Rfree (for highest resolution shell)

[Smith Lee]

Dear Pavel,
Once the Ramachandran outliers (and the rotamer outliers) was corrected by coot, another round of Phenix refine usually cause the rising of the Rwork and Rfree. Is any way to avoid this rising? After this Rwork and Rfree rising, can I continue the refinement with the Rwork and Rfree rising PDB and MTZ files to try to lower the Rwork and Rfree?
Smith

 

     On Tuesday, January 27, 2015 3:28 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
   

  George,
 
 what exactly you are trying to achieve by making sense of Rfree and its relation to Rwork in resolution shells? Just curious..
 
 Pavel
 
 On 1/26/15 1:50 PM, George Devaniranjan wrote:
  
 Thank you Tim and Pavel. 
  Sorry, just to follow up: 
  For the example I gave R /Rfree difference seems high. Can this still be down to statistical fluctuations? 
   I am just trying to get a feel when we can simply put it down to statistical fluctuations and when its a concern. 
   
 On Mon, Jan 26, 2015 at 4:26 PM, Tim Gruene <tg at shelx.uni-ac.gwdg.de> wrote:
 
Dear George,
 
 you may also want to take into account that the variation of Rfree is
 estimated as Rfree^2/k, where k is the number of reflections in the
 shell. If you only have e.g. 100 reflections there, this might simply a
 statistical fluctuation, as far as I understand.
 
 Cheers,
 Tim
 
 On 01/26/2015 10:05 PM, George Devaniranjan wrote:
 > Hi,
 >
 > I calculated/validated several PDB structures in Phenix.Validation (GUI)
 >
 > The R/R-free (overall) is
 >
 > 0.1271/0.1348
 >
 > Further down I looked at the R/R-free for the highest resolution shell.
 >
 > Its 0.2538/0.2446
 >
 > I am curious why the R-free for the *highest resolution shell* seems to be
 > LOWER than R (work).
 >
 >
 > Am I reading the information wrong?
 >
 > PDB: 3QL9
 >
 > Thank you,
 > George
 >
 >
 >
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   --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
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