[phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

Nathaniel Echols nechols at lbl.gov
Thu May 30 07:26:53 PDT 2013

On Thu, May 30, 2013 at 7:09 AM, Heather Condurso <condurso at bc.edu> wrote:
> I have a similar issue.  My data is nearly perfectly twinned so Xtriage usually fails to find any twin law.  However when I solve the structure in the lower symmetry space group with twinning my maps look beautiful.  In the higher symmetry space group, only 3 of the 6 monomers fit into nice looking density.  I simply use generate table 1 and uncheck the box so it won't regenerate R factors.  The discrepancy between the R-factors is however much more significant than 2%.  From refine I get 18/22 and from table1 28/31.

That's actually a little surprising that Xtriage wouldn't work - would
you be willing to send us the data?  Keep in mind that if you have
perfect twinning and refine with the twin law, I think the maps will
look beautiful pretty much by definition, because of the model bias.
(Which doesn't mean that you did it wrong - the R-factors sound
realistic - you just need to be very careful and make lots of omit

It helps to have actual examples when warning against the dangers of
twin refinement and model bias in general, so here's one (attached).
This map isn't beautiful, but it matches the model very closely,
including the complete lack of sidechains.  Another Phenix user got
this result by accident with a mostly-if-not-entirely incorrect MR
solution - fortunately the combination of missing sidechain density
and relatively high R-free (~40%) prompted him to email us.  I suspect
that if we searched the PDB we'd find an actual published example
(especially considering how many spurious ligands have been found

(Sorry to sound like a broken record here, but this keeps coming up in
emails and workshops - perhaps we need better validation tools.)

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