[phenixbb] phenix refinement question

Pavel Afonine pafonine at lbl.gov
Mon Nov 15 13:50:06 PST 2010


>> I have only started using PHENIX and have made an interesting observation.
>> If I run my model through PHENIX refine (individual sites, individual ADPs,
>> occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP
>> weight options selected) I obtain R/Rfree 0.15/0.18 and very nice geometry
>> values (data is to 1.7A). However, if I now take this refined model and run
>> it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21.

sounds good to me, I would be worried otherwise.

>> Can anyone explain why is there such a big difference? Will this be an issue
>> during PDB submission?

Have a look at this:

J. Appl. Cryst. (2010). 43, 669-676
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 
and P. D. Adams

> Take a look at what phenix.refine reports for the number of
> reflections used for refinement in the logfile - I believe it will
> discard reflections that are flagged as suspicious (can't remember the
> reference, I think it's one of Randy Read's papers),

It is typically from zero to a few dozens of reflections and unless they 
are ~1.e+9 removing them rarely visible in terms of R-factor (if you 
just re-compute it).


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