[phenixbb] CB outliers

Nathaniel Echols nechols at lbl.gov
Fri Nov 7 08:35:06 PST 2014

On Fri, Nov 7, 2014 at 2:08 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Phenix.refine uses CB restraints by default, so unless you disabled it or
> your model is very poor, you should not have these outliers after
> refinement (again, normally).

Why is this enabled by default?  CB outliers are diagnostic for other
errors in the model, like the scenario of the partially-split sidechain I
described.   This is the reason why they're the only chiral centers flagged
in MolProbity.  If the rest of the atoms in the residue are compatible with
a proper CB position, the standard geometry restraints should be sufficient
to keep it there.  If not, adding more restraints will either introduce
other errors into model geometry, or mask the actual problem with the
model.  Either way, this is not actually going to lead to better structures.
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