The error occurs because you're the actual flags used in refinement have changed due to the resolution being extended.  As the error message notes, this is nothing to be worried about, so you can simply delete that REMARK line and continue with refinement.

(Note that even if the flags already went to 3.0Å with the old data, you only used a subset of them to 3.5Å, and I assume that's what is used to calculate the checksum.)


On Fri, Oct 11, 2013 at 6:32 AM, S. Saif Hasan <sshasan@purdue.edu> wrote:
Hello,

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:
  2ee90dd0a36800bb94370f83daf01698

The corresponding MD5 checksum in the PDB file summarized above is:
  2e1cdfda59def2c4fb80ea6f1e452566

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.

Saif
Purdue University


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