<html>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Ezequiel,<br>
<br>
version: dev-2247: Final: r_work = 0.1753 r_free = 0.2040<br>
vs <br>
version: dev-2247: Final: r_work = 0.1663 r_free = 0.2017<br>
<br>
look the same in a sense that if you 100 refinements each one
starting with a slightly perturbed model you will get 100 slightly
different refined models with both, Rwork and Rfree, varying withing
about 1% at this resolution. Having said that I can postulate that
r_work = 0.1753 is the same as r_work = 0.1663, and r_free = 0.2040
is the same as r_free = 0.2017.<br>
<br>
For some discussion see pages 75-77 here:<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf">http://phenix-online.org/presentations/latest/pavel_refinement_general.pdf</a><br>
and<br>
"Improved target weight optimization in phenix.refine" here:<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/newsletter/CCN_2011_07.pdf">http://phenix-online.org/newsletter/CCN_2011_07.pdf</a><br>
<br>
Now, before I proceed commenting, question: did you follow exactly
the steps 1)-2)-3) that I outlined in my previous email? Otherwise
it does not make much sense to compare results obtained using
different refinement settings.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 12/15/15 12:00, Ezequiel Noguera
wrote:<br>
</div>
<blockquote
cite="mid:714336546.1353914.1450209611428.JavaMail.yahoo@mail.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff;
font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial,
Lucida Grande, sans-serif;font-size:16px">
<div id="yiv7446656312">
<div id="yui_3_16_0_1_1450197484812_7406">
<div id="yui_3_16_0_1_1450197484812_7405"
style="color:#000;background-color:#fff;font-family:HelveticaNeue,
Helvetica Neue, Helvetica, Arial, Lucida Grande,
sans-serif;font-size:16px;">
<div id="yiv7446656312yui_3_16_0_1_1450133203464_3271">
<div id="yui_3_16_0_1_1450197484812_7704">Thank you very
much, Pavel. I don't save H's when I modify the model
in coot (the input PDB file that I sent you was the
output from coot). I did the refinement again, now in
version 2247, without NCS. I got the same results,
higher R factors and RMS deviations for the newer
version. I got better results when I used "update
waters" (both in Rfactors and RMS). Below, I list the
statistics for refinement without updating waters.
Significant differences remain. Could it be any
difference in settings of default parameters between
versions?<br>
</div>
<div dir="ltr" id="yui_3_16_0_1_1450197484812_7801">version:
dev-2247<br>
</div>
<div dir="ltr" id="yui_3_16_0_1_1450197484812_7735">Start:
r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles =
1.321<br class="" id="yui_3_16_0_1_1450197484812_7799">
Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030
angles = 0.593<br>
</div>
<div id="yui_3_16_0_1_1450197484812_7686" dir="ltr">version:
1.9-1692<br>
</div>
<div id="yui_3_16_0_1_1450197484812_7702" dir="ltr">Start:
r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles =
1.409<br class="" id="yui_3_16_0_1_1450197484812_7685">
Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011
angles = 1.321<br>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</body>
</html>