[phenixbb] phenix refinement question

Steiner, Roberto roberto.steiner at kcl.ac.uk
Tue Nov 16 00:06:12 PST 2010

Dear Katarina

I would suggest you post the same question to the CCP4bb and hopefully Refmac users/experts will comment on this. It is always very difficult to understand what's going on without having a look at input/output files.

Best wishes

From my iPhone

On 15 Nov 2010, at 23:25, "Katarina Moravcevic" <katarinm at mail.med.upenn.edu<mailto:katarinm at mail.med.upenn.edu>> wrote:

Hi Pavel,
after reading the paper you suggested I have to admit I am still confused with this discrepancy. In the section that describes specific reasons in R/Rfree discrepancies that could apply to my model, REFMAC and PHENIX supposedly use same principles. So, do these differences come from some slight variations in how for example bulk solvent and anisotropic scaling are treated in two programs?
I am sorry for asking basic questions and please do not bother to reply if it is too silly.

On Mon, Nov 15, 2010 at 4:50 PM, Pavel Afonine <<mailto:pafonine at lbl.gov>pafonine at lbl.gov<mailto:pafonine at lbl.gov>> wrote:

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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