[phenixbb] R value difference in model vs data vs refinement

[Ralf Grosse-Kunstleve]

The R-factor difference of 0.0004 is what you have to expect as the result
of writing the coordinates, B-factors, and occupancies to the PDB file. In
memory floating-point numbers have >= 12 digits precision (we use double
precision for almost everything); in the PDB file you have only 7 digits
for the coordinates and just 5 digits for the B-factors and occupancies.
Ralf

On Fri, Mar 23, 2012 at 9:49 AM, Christian Roth <
christian.roth at bbz.uni-leipzig.de> wrote:

> Hi Nat,
>
> I agree with you that the difference is very small and likely negligible. I
> just asked for curiosity if there might be any reason for this behaviour.
>
> Christian
>
> Am Donnerstag 22 März 2012 23:07:33 schrieb Nathaniel Echols:
> > On Thu, Mar 22, 2012 at 2:54 PM, Christian Roth
> >
> > <christian.roth at bbz.uni-leipzig.de> wrote:
> > > I am not sure I looked into the polygon. In the log it is stated that
> the
> > > R values are calculated after a resolution and sigma cutoff applied.
>  If
> > > I understood the log correctly the values taken from the pdb header are
> > > without sigma cutoff. Maybe thats the reason for the difference. Does
> > > modelvsdata somewhere print the values without cutoff in the log file?
> I
> > > did not find it. However does this mean till firsst OHS in phenix
> refine
> > > a default cutoff is used and in than throughout the refinement no
> coutoff
> > > is used anymore?
> >
> > After spending some time looking at similar cases today I am not sure
> > myself what is going on.  I do not think a sigma cutoff is applied,
> > unless perhaps the PDB header indicates that one was used previously
> > (this is a thoroughly antiquated practice).  However, outlier
> > filtering appears to be used throughout.  I found one example where
> > nearly 4000 reflections have amplitudes of zero (which is surely not
> > correct), and are discarded as outliers in phenix.refine.  This
> > reduces R-free by 0.03.  In model_vs_data, the same numbers appear
> > twice:
> >
> >   Model_vs_Data:
> >     r_work(re-computed)                : 0.2030
> >     r_free(re-computed)                : 0.2639
> > ...
> >   After applying resolution and sigma cutoffs:
> >     n_refl_cutoff : 31257
> >     r_work_cutoff : 0.2030
> >     r_free_cutoff : 0.2639
> >
> > But this totally contradicts what I told you earlier, sorry.  I was
> > assuming that they would be different.
> >
> > I do have a general piece of advice, however: ignore the discrepancy,
> > and just report the value that came out of refinement (because that is
> > what will end up in the PDB).  The difference in your case is
> > relatively small, probably less than what you'd see if you calculated
> > R-factors with (for instance Refmac), because of different
> > implementations of bulk solvent correction and scaling, etc.*.  (Even
> > different versions of Phenix aren't guaranteed to yield identical
> > R-factors, due to low-level changes.)  Considering how difficult it
> > can be to reproduce the statistics in published structures, a change
> > of 0.0004 isn't enough to worry about.
> >
> > -Nat
> >
> > * http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906258/?tool=pubmed
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> >
>
>
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