<div dir="ltr">On Fri, Nov 7, 2014 at 2:08 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">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).</div></blockquote><div><br></div><div>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.</div></div></div></div>