[phenixbb] observed reflection numbers of refinement greater than the experiment

[Ralf W. Grosse-Kunstleve]

>   Actually, I didn't do any anomalous refinement by phenix.refine. I only used the default option.
>    
>   i checked the log file after refinement, it seems that the annomalous flag is true. But i don't clear the anomalous be used or not.

If your input data are anomalous, phenix.refine keeps F+ and F-
separate during refinement.
You can change this via:

  xray_data.force_anomalous_flag_to_be_equal_to=False

Usually it doesn't make much of a difference for the end results, but
I'd try and go with the better R-free.

>   If yes, how i can report the number of observed reflections of refinment when PDB deposition. 
>   I know the number of reflections for refinement and experiment should be the number of all reflections which contains Friedel pairs.

phenix.refine writes the number of reflections used in refinement into
the pdb header (REMARK   3   NUMBER OF REFLECTIONS).
(It may not match the number of reflections in the original file, but
that's expected.)

>   How i can make the SF file contains the Friedel pairs?

I think you can directly deposit the <prefix>_data.mtz file written
by phenix.refine.

Ralf