[phenixbb] R/R free reported values

[George Devaniranjan]

Hi Nat,

Would you define "significant" for me (as you see it of course)?

I am NOT a X-ray crystallographer but I was intrigued by this post. I have
RE-refined structures and have seen R/R (Free) go up say by 0.4
Say from 0.110 to 0.150
Would you say that is significant for high resolution structures ?

Thank you,
George

On Mon, Oct 27, 2014 at 4:13 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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
> says:
>
>     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.
>
> -Nat
>
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