[phenixbb] Free-R flag error

S. Saif Hasan sshasan at purdue.edu
Fri Oct 11 06:32:29 PDT 2013


I am refining a 3.0 A data set. Initially, I calculated the map at 3.5 A. I have now extended the resolution to 3.0 A, and I imported the FreeR-flags into the 3.0 A .sca file from the 3.5 A file. When I use the 3.0 A .mtz file, phenix.refine gives me this error- 
The MD5 checksum for the R-free flags array summarized above is:

The corresponding MD5 checksum in the PDB file summarized above is:

These checksums should be identical but are in fact different. This is
because the R-free flags used at previous stages of refinement are
different from the R-free flags summarized above. As a consequence,
the values for R-free could be biased and misleading.

However, there is no problem if the R-free flags were just extended to
a higher resolution, or if some reflections with no data or that are
not part of the R-free set have been added or removed. In this case,
simply remove the

  REMARK r_free_flags.md5.hexdigest 2e1cdfda59def2c4fb80ea6f1e452566

record from the input PDB file to proceed with the refinement. 

Otherwise it is best to recover the previously used R-free flags
and use them consistently throughout the refinement of the model.
Run this command again with the name of the file containing the
original flags as an additional input.
Why does phenix.refine give me this message when I have imported the FreeR-flags from the low resolution file? And what should I do about fixing it?

Thank you for all suggestions.

Purdue University

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