[phenixbb] Validation question: R-factor (all) and # of unique reflections (all)

Pavel Afonine pafonine at lbl.gov
Tue Jul 5 11:45:25 PDT 2011

Hi Young-Jin,

> While I am trying to deposit, I am faced with several things that I am 
> not sure: FYI. I am in the <Refinement Statistics> section (Auto Dep 
> Input Tool) in the PDB bank.
> Most values are came from pdb file that was made from phenix.refine 
> but it asks me "R-factor (all)" that satisfy the limits established by 
> high & low resolution cut off and "number of unique reflections (all)".
> My simple question is if phenix has those kind of information, if so 
> where I can find them.

phenix.refine and phenix.model_vs_data report Rfree and Rwork computed 
for all reflections used in refinement (which may be different from the 
number of reflections in your input file, because of Iobs to Fobs 
conversion and outliers filtering). They do not report R(all) since I 
believe it is a useless number given that both, Rfree and Rwork, are 

If you really want it you can compute it using a MTZ file created by 
phenix.refine, since it contains Fobs used in refinement and Fmodel, so 
the R-factor is simply

R = SUM ||Fobs|-scale*|Fmodel|| / SUM |Fobs|


scale = SUM ( |Fobs|*|Fmodel| )/SUM |Fmodel|**2

> Another question is if I changed water (deletion or changed occupancy) 
> based on 'precheck', should I run phenix.refine again to get R/Rfree 
> values in correct? 

Yes, definitely, preferably with "ordered_solvent=true" flag. And having 
a look at this paper:

phenix.model_vs_data: a high-level tool for the calculation of 
crystallographic model and data statistics. P.V. Afonine, R.W. 
Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, 
D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 
43, 677-685 (2010).

is also a good idea in this case, since it explains how bad a 
post-refinement manipulation of PDB or data files can be.

All the best!

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