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The problem of all these metrics is that they are binary: YES
(=outlier) or NO (=not an outlier).<br>
<br>
You may be 1.e-5 or so (just making up a number) away from NO but
the program may still consider it as outlier. And obviously you will
not see that different on graphics (in Coot for instance).<br>
<br>
This is exactly why I don't particularly like functions with kinks
and instead prefere smoothly differentiable ones!<br>
<br>
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).<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 11/5/14 11:43 AM, George
Devaniranjan wrote:<br>
</div>
<blockquote
cite="mid:CAFU65Pfq5TZM0t4P3-HcfCSniKJbbd1McY0zvkxq1yoTmJ6sCw@mail.gmail.com"
type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>�I refined a structure using phenix.refine.<br>
</div>
<div><br>
</div>
<div>The R/R free decreased slightly from 13.46/15.87 to
13.0/15.6.</div>
<div><br>
</div>
<div>But, molprobity said there were 3 CB outliers (starting
from 0).</div>
<div><br>
</div>
<div>I looked at those residues in COOT. I could NOT really see
a different between the refined and initial model.</div>
<div><br>
</div>
<div>In addition I looked at COOT</div>
<div>validate-->density fit analysis</div>
<div>I cannot see ANY difference in the peak heights (same
numerical value too).</div>
<div><br>
</div>
<div>I looked at RSCC (using phenix validate tools as well).</div>
<div>I still can't see a difference in the plots.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>I ask since in another case > 3 CB outliers, with the
same results in picking them out in COOT/RSCC.</div>
<div><br>
</div>
<div>I am wondering if there is another way I can see the
deviation and fix it?</div>
<div><br>
</div>
<div>Thank you,</div>
<div>George</div>
</div>
<br>
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