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Hi Smith,<br>
<br>
Phenix version 1.10.1 (the latest official) is the one to use, and
by design it is supposed to be superior than previous versions.
Actually this is what you confirm with your results: with 1.10.1 you
get better model (less Ramachandran plot outliers, similar other
metrics) and better model-to-map fit (CC =0.761 vs 0.687).<br>
<br>
It is not clear to me why you find the model from 1.10.1 version
unacceptable.<br>
<br>
I suggest you to find a handful of most severe steric clashes and
resolve them.<br>
<br>
Pavel<br>
<br>
<blockquote
cite="mid:617681169.2217511.1445183739896.JavaMail.yahoo@mail.yahoo.com"
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<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4291"
dir="ltr">Today I just completed another protein
phenix.real_space_refine. For the following comparison
runs, the initial model same, the map same, all 5
macro_cycles default run.</div>
<div class="yiv4854416411qtdSeparateBR"
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<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4240"
dir="ltr">For version 1.10.1, the results were as
following,</div>
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id="yiv4854416411yui_3_16_0_1_1445174093830_4243"
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<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4252"
dir="ltr">Map CC (whole unit cell)： 0.672</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4276"
dir="ltr">Map CC （around atoms）： 0.761</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4304"
dir="ltr">rmsd （bonds): 0.01</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4340"
dir="ltr">rmsd (angles): 1.55</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4377"
dir="ltr">All-atom clahscore: 39.27</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4404"
dir="ltr">Ramachandran outlier: 0.98%</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4428"
dir="ltr">Ramachandran allowed: 12.71%</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4473"
dir="ltr">Ramachandran favoured: 86.31%</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4460"
dir="ltr">Rotamer outliers: 0.91%</div>
<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4492"
dir="ltr">C-beta deviations: 0</div>
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id="yiv4854416411yui_3_16_0_1_1445174093830_4553"
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<div class="yiv4854416411qtdSeparateBR"
id="yiv4854416411yui_3_16_0_1_1445174093830_4554"
dir="ltr">For version 1.9-1692, the results were as
following,</div>
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id="yiv4854416411yui_3_16_0_1_1445174093830_4576"
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<div id="yiv4854416411yui_3_16_0_1_1445174093830_4252"
dir="ltr">Map CC (whole unit cell)： 0.645</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4276"
dir="ltr">Map CC （around atoms）： 0.687</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4304"
dir="ltr">rmsd （bonds): 0.0071</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4340"
dir="ltr">rmsd (angles): 1.15</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4377"
dir="ltr">All-atom clahscore:16.88</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4404"
dir="ltr">Ramachandran outlier: 2.00%</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4428"
dir="ltr">Ramachandran allowed: 6.23%</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4473"
dir="ltr">Ramachandran favoured: 91.77%</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4460"
dir="ltr">Rotamer outliers: 0.05%</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4492"
dir="ltr">C-beta deviations: 0</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4686"
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</div>
<div id="yiv4854416411yui_3_16_0_1_1445174093830_4685"
dir="ltr">For the version 1.10.1
phenix.real_space_refine, the most unacceptable was on
the clashscore, the whole refine process seems did
not care on the clashcore refine at all.</div>
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<div id="yiv4854416411yui_3_16_0_1_1445174093830_4735"
dir="ltr">I am looking forward to getting an
explanation from you on the causes of the difference for
phenix.real_space_refine for the 2 versions, and the
possible strategy we can take to eliminate the
difference to get the acceptable results.</div>
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<div id="yui_3_16_0_1_1445183640836_2378" dir="ltr">Best
regards.</div>
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clear="none">
</div>
<div dir="ltr">Smith </div>
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<div class=".yiv4854416411yahoo_quoted">
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<div id="yiv4854416411yui_3_16_0_1_1445174093830_4162"
dir="ltr"> <font
id="yiv4854416411yui_3_16_0_1_1445174093830_4161"
face="Arial" size="2"> On Friday, October 9, 2015
12:52 AM, Smith Lee <a class="moz-txt-link-rfc2396E" href="mailto:smith_lee123@yahoo.com"><smith_lee123@yahoo.com></a>
wrote:<br clear="none">
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id="yiv4854416411yui_3_16_0_1_1445174093830_4168">
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<div id="yiv4854416411yui_3_16_0_1_1445174093830_4167">
<div
id="yiv4854416411yui_3_16_0_1_1445174093830_4166"
style="color: rgb(0, 0, 0); font-family:
HelveticaNeue, Helvetica Neue, Helvetica, Arial,
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background-color: rgb(255, 255, 255);">
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7108">
Dear Pavel，</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7109"><br
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<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7110"
dir="ltr">As I have told you, I have tried
phenix.real_space_refine for 2 protein with
version 1.9-1692 and version 1.10 (and 1.10.1)
for many times, with cif or without cif, with or
without annealing. The general feedback was that
the version 1.9-1692 was much much better for
the final analysis of the PDB given at the end
of the run of the phenix.real_space_refine.
Especially for clashing score, version 1.9-1692
can gave acceptable results (below 20 or around
20), but the clashing score given by the above 2
new versions of phenix.real_space_refine was
very high (around 50 or 100). For
C-beta deviations, the output by 1.9-1692 was
also much better</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7252"
dir="ltr"><br clear="none">
</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7253"
dir="ltr">Before I have tried the other nightly
built versions of phenix.real_space_ refine
between version 1.9-1692 and version 1.10 (and
1.10.1) , all I gave acceptable output analysis
(something like the Molprobity analysis at the
end of the run).</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7321"
dir="ltr"><br clear="none">
</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7322"
dir="ltr">Thus may I ask the reason you have
version 1.10 (and 1.10.1)
phenix.real_space_refine was because you have
realized that the result given by version
1.9-1692 was too satisfactory?</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7348"
dir="ltr"><br clear="none">
</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7349"
dir="ltr">One direct concern of me was that you
have recommended not to use the old version
phenix. But I cannot get the satisfactory result
with the new version phenix.real_space_refine.</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7397"
dir="ltr"><br clear="none">
</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7396"
dir="ltr">The other concern of me was that, I
have noticed there were publications In Nature
and Science which wrote they use
phenix.real_space_refine to got the results in
Nature and Science. The Phenix they used should
be the versions earlier than version 1.10.
Considering what I mentioned above, the Nature
and Science results may be not so correct, if
new version of phenix was considered as much
better than the old version.</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7458"
dir="ltr"><br clear="none">
</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7434"
dir="ltr">Thus am I the only user who
communicated with you on the high clashing score
given by the new version of phenix？Can you give
some comments on what I mentioned above on the
high clashing score given by the new version
phenix.real_spac_refine?</div>
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id="yiv4854416411yui_3_16_0_1_1444285745936_7467"
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<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7466"
dir="ltr">Best regards.</div>
<div dir="ltr"><br clear="none">
</div>
<div dir="ltr"><br clear="none">
</div>
<div dir="ltr">Smith</div>
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id="yiv4854416411yui_3_16_0_1_1444285745936_7449"
dir="ltr"><br clear="none">
</div>
<div
id="yiv4854416411yui_3_16_0_1_1444285745936_7450"
dir="ltr"> </div>
</div>
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