[phenixbb] R/R free reported values

Nathaniel Echols nechols at lbl.gov
Mon Oct 27 13:13:59 PDT 2014

On Mon, Oct 27, 2014 at 1:00 PM, Cedric <patrick.cossins at inbox.com> wrote:

> Hi Phenix and CCP4 community,
> (sorry for the cross posting).
> I was looking at a PDB file.
> The http://www.rcsb.org/ website page gives the following values:
> R-Value: 0.103 (work)
> R-Free:  0.134
> The actual PDB file gives the following:
> R :0.110
> FREE R VALUE : 0.170
> I was wondering why the difference. The structure is 1.0A resolution 2CWS.

I don't have an exact explanation, but there is some inconsistency in the
way data are stored internally by the PDB.  The mmCIF file is the most
complete representation:

_refine.ls_R_factor_R_work                     0.103
_refine.ls_R_factor_R_free                     0.134
_pdbx_refine.R_factor_all_no_cutoff                      0.1101
_pdbx_refine.R_factor_obs_no_cutoff                      ?
_pdbx_refine.free_R_factor_no_cutoff                     0.1704

So, the first set is what gets displayed on the web page, the second set
ends up in the PDB header.  I suspect something went awry in deposition,
but only the PDB and the depositors can answer that question.

I wouldn't take the advertised statistics at face value anyway; I prefer to
rely on recalculated values (and if these are significantly different, I
view the structure with suspicion).  In this case, phenix.model_vs_data

    r_work(re-computed)                : 0.1081
    r_free(re-computed)                : 0.1377

which, accounting for the precision loss in PDB format and the differences
between SHELXL and Phenix, are reasonable enough, and suggest that the
values on the web page are probably accurate.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20141027/78a9b359/attachment.htm>

More information about the phenixbb mailing list