[phenixbb] CB outliers

Pavel Afonine pafonine at lbl.gov
Fri Nov 7 11:09:06 PST 2014

Hi Nat,

It is enabled by default because it is as equal piece of information as 
restraints on lengths of covalent bonds, values of covalent angles and 
all other restraints. It is simply extra information that would be shame 
to not use actively especially if it comes for free, and is trivial to 
define unambiguously (unlike Ramachandran restraints, for instance).

I've made it default perhaps a year ago and I've not seen any problem 
related to this since then. I can demonstrate improvements in 
low-resolution real-space refinement when using CB restraints vs not 
using them, for example.
If you can bring an example that proofs your concerns (that is clearly 
shows that using these restraints is counterproductive) I will be happy 
to investigate!

As to diagnostics, I think proper use of existing metrics such as local 
(per atom) 2mFo-DFc and mFo-DFc map fit, along with local standard 
geometry quality metrics (clashes, deviations from ideal targets, etc) 
should be totally sufficient to identify problems.


On 11/7/14 8:35 AM, Nathaniel Echols wrote:
> On Fri, Nov 7, 2014 at 2:08 AM, Pavel Afonine <pafonine at lbl.gov 
> <mailto: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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