[phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

Sam Stampfer Samuel.Stampfer at tufts.edu
Wed May 29 16:13:39 PDT 2013

Dear Phenix Community,

I am preparing my structure for deposition and ran it through the Generate
"Table 1" function in phenix. The inputs I gave it were my .mtz structure
factors file, the final pdb coordinate file, and the log file from hkl2000.
I did not provide unmerged data.

My pdb file (which had been refined using phenix.refine) had values of
r_work=0.2342 r_free=0.2603
However, phenix.model_vs_data (from Generate "Table 1") gave me
r_work=0.2940 r_free=0.3150

I also got this warning about resolution limits, but I think it should not
have affected the R-free calculation to this extent:
WARNING: Resolution limits in scaling log for structure
             are inconsistent with resolution limits in the MTZ file:
             50.00 - 3.02 (in logfile)
             48.47 - 3.03 (in MTZ file)

When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in
the documentation that twinning can account for some of this discrepancy,
but that the program is supposed to take twinning into account if it will
lower the calculated R-work by more than 2%, which it doesn't seem to have
done (or there is some other problem with my data).

Thanks for your help!

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