[phenixbb] question about phenix.refine

crystallogrphy qunwan1 at gmail.com
Thu Sep 3 14:43:41 PDT 2009

I want to use phenix to refine a model right after autobuild with the
following script:
phenix.refine xray_data.file_name=exptl_fobs_phases_freeR_flags.mtz
overall_best-090903a.pdb strategy=rigid_body+individual_sites
simulated_annealing=true simulated_annealing.start_temperature=8000
sites.rigid_body="chain A" sites.rigid_body="chain B"

However, the program says "

If previously used R-free flags are available run this command again
with the name of the file containing the original flags as an
additional input. If the structure was never refined before, or if the
original R-free flags are unrecoverable, run this command again with
the additional definition:


when I use phenix.mtz.dump exptl_fobs_phases_freeR_flags.mtz, it indicates
that it has FreeR_flag=1. Can anyone tell me why there is FreeR_flag in my
data, while the refinement program does not recognize it?
  label      #valid  %valid    min    max type
    H           35619 100.00%   0.00  22.00 H: index h,k,l
    K           35619 100.00%   0.00  45.00 H: index h,k,l
    L           35619 100.00% -33.00  33.00 H: index h,k,l
    FP          35619 100.00%   0.00 114.22 F: amplitude
    SIGFP       35619 100.00%   0.15   6.13 Q: standard deviation
    PHIM        35619 100.00%   0.00   0.00 P: phase angle in degrees
    FOMM        35619 100.00%   0.00   0.00 W: weight (of some sort)
    FreeR_flag  35619 100.00%   0.00   1.00 I: integer
    FC          35619 100.00%   0.00   0.00 F: amplitude
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