[phenixbb] Free-R flag error

Nathaniel Echols nechols at lbl.gov
Fri Oct 11 08:41:49 PDT 2013

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 at 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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