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Hi Nat,<br>
<br>
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).<br>
<br>
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. <br>
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!<br>
<br>
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.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 11/7/14 8:35 AM, Nathaniel Echols
wrote:<br>
</div>
<blockquote
cite="mid:CALeAa1OD4YK-kp5Rbmctgrma3ptkPs9jcc9AqJxzn93hGrwt5g@mail.gmail.com"
type="cite">
<div dir="ltr">On Fri, Nov 7, 2014 at 2:08 AM, Pavel Afonine <span
dir="ltr"><<a moz-do-not-send="true"
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>
</blockquote>
<br>
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