[phenixbb] CB outliers

Nathaniel Echols nechols at lbl.gov
Wed Nov 5 12:25:47 PST 2014

The program KiNG (which can be launched from the validation GUI, and is
also available via the MolProbity server) will display the CB outliers
graphically - represented by a sphere, the radius of which indicates the
displacement from ideal position.

Since this is obviously a very high resolution structure, the first thing
to check is whether these residues are in alternate conformations.  It is
quite common (although almost always wrong) for disordered residues to be
split starting at CB, i.e. assuming that the mainchain is rigid and only
the sidechain atoms differ between conformations.  This tends to lead to CB
outliers, because the mainchain actually needs to be flexible as well.  It
is much better to simply split the entire residue, regardless of how much
you think the mainchain needs to move; by the time you can see clear
alternate conformations you usually have so much data that the extra
parameters won't be a problem.  (It's often a good idea to split the
adjacent residues as well, since their backbones may also need to flex a
little bit to accommodate the central residue.)

On Wed, Nov 5, 2014 at 11:43 AM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi,
>  I refined a structure using phenix.refine.
> The R/R free decreased slightly from 13.46/15.87 to 13.0/15.6.
> But, molprobity said there were 3 CB outliers (starting from 0).
> I looked at those residues in COOT. I could NOT really see a different
> between the refined and initial model.
> In addition I looked at COOT
> validate-->density fit analysis
> I cannot see ANY difference in the peak heights (same numerical value too).
> I looked at RSCC (using phenix validate tools as well).
> I still can't see a difference in the plots.
> I am not sure how to get rid of the 3 CB outliers that have crept in since
> I can't pick them out as worse off in the refined model.
> I ask since in another case > 3 CB outliers, with the same results in
> picking them out in COOT/RSCC.
> I am wondering if there is another way I can see the deviation and fix it?
> Thank you,
> George
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