[phenixbb] CB outliers

George Devaniranjan devaniranjan at gmail.com
Fri Nov 7 08:41:38 PST 2014

Thank you both for your replies.

@Nataniel-thank you, I will look into King.

@Pavel -I was experimenting with NO restraints (since this was 0.8A
structure) and as you suggested the deviations though 3 were barely "out".
I asked the question more since I could not see the difference in COOT
density fit.
Just to clarify, when you say restraints, you are talking about wxc right?

On Fri, Nov 7, 2014 at 11:35 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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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