<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Wolfram,<br>
<br>
<blockquote type="cite"
cite="mid:CAGjFzmBUCUCZUgHjF8tX3omHzO28Sn6stkDNNOzyq0kvrH88bA@mail.gmail.com">
<div dir="ltr">
<div class="markdown-here-wrapper" style="">
<p style="margin:1.2em 0px!important">Hello all,<br>
the <a
href="https://www.phenix-online.org/documentation/faqs/refine.html">documentation</a>
states that</p>
<blockquote style="margin:1.2em 0px;border-left:4px solid
rgb(221,221,221);padding:0px
1em;color:rgb(119,119,119);quotes:none">
<p style="margin:1.2em 0px!important">This is somewhat
controversial, but absolute upper limits for a
well-refined protein structure at high resolution are
typically 0.02 for RMS(bonds) and 2.0 for RMS(angles);
usually they will be significantly lower.</p>
</blockquote>
<p style="margin:1.2em 0px!important">I understand that
exceedingly high RMSDs from ideal could indicate
overfitting.<br>
On the other hand, local deviations from ideal geometry may
point to correctable modeling errors, and I am concerned
that overly tight restraints may cause that diagnostic tool
to become less sensitive, or local errors to be spread in to
the model.<br>
</p>
</div>
</div>
</blockquote>
<br>
Do you have an example? I've heard this many times but so far nobody
could show me a convincing example that demonstrates how tighter
bond/angle restraints mask "other problems". <br>
Also, looking at just bond/angles rmsds from ideal library values
isn't comprehensive and may indeed lead to some problems being
overlooked. Using all arsenal of validation tools, global and local,
should find most problems.
<blockquote type="cite"
cite="mid:CAGjFzmBUCUCZUgHjF8tX3omHzO28Sn6stkDNNOzyq0kvrH88bA@mail.gmail.com">
<div dir="ltr">
<div class="markdown-here-wrapper" style="">
<p style="margin:1.2em 0px!important">For what bond and angle
rms deviations from ideal do my colleagues on the BB aim and
how have they arrived at those targets? <br>
</p>
</div>
</div>
</blockquote>
See Jaskolski et al., 2007; Wlodawer et al., 2008; Stec, 2007;
Tickle, 2007; Karplus et al., 2008 and references inside.<br>
<br>
Pavel<br>
<br>
</body>
</html>