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Hi Ezequiel,<br>
<br>
just to make it clear: torsion-angle NCS, Optimize X-ray/stereo
weight are *not* the default settings, therefore you did customize
the refinement parameters.<br>
<br>
At this resolution (1.3A) you do not need to use NCS restraints. <br>
<br>
Also, you say you used "<span style="font-family: 'Helvetica Neue',
'Segoe UI', Helvetica, Arial, 'Lucida Grande', sans-serif;
font-size: 13px;" class="" id="yui_3_16_0_1_1449410509620_9048">Automatically
add H's</span>" however the PDB file you sent me does not contain
any H atoms. Furthermore, the PDB file header says H are present:<br>
<br>
REMARK MODEL
CONTENT. <br>
REMARK ELEMENT ATOM RECORD COUNT OCCUPANCY
SUM <br>
REMARK C 1275
1047.00 <br>
<b>REMARK H 2029
1649.00 </b><br>
REMARK O 559
488.50 <br>
REMARK N 315
263.00 <br>
REMARK S 6
6.00 <br>
REMARK Cu 4
2.89 <br>
REMARK TOTAL 4188
3456.39 <br>
<br>
So overall this make an impression that something has gone wrong.<br>
<br>
Way forward:<br>
<br>
1) Take the file you sent me;<br>
<br>
2) Add H atoms:<br>
<br>
phenix.reduce model_no_h.pdb > model_with_h.pdb<br>
<br>
3) Use new file with H atoms added to run refinement. The only
setting different from defaults should be "Optimize X-ray/stereo
weight". Perhaps you can also enable automated water update.<br>
<br>
I just did all this myself and got nicely refined model with <br>
<br>
Final: r_work = 0.1624 r_free = 0.1939 bonds = 0.010 angles = 1.030<br>
<br>
Corresponding PDB and MTZ are sent in a separate email that goes to
you only (off mailing list).<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/6/15 07:59, Ezequiel Noguera
wrote:<br>
</div>
<blockquote
cite="mid:1707157291.13122695.1449417590877.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="yui_3_16_0_1_1449410509620_8892" class="" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
class="" id="yui_3_16_0_1_1449410509620_9048">Hi Pavel,
thank you very much for your help. I attach the data. I
didn´t customize parameters. The refinement stategy of the
last job was: XYZ coords, Real-space, Individual B-factors,
torsion-angle NCS, Optimize X-ray/stereo wght and X-ray/ADP
wght, Automatically add H's and correct N/Q/H errors.</span></div>
<div id="yui_3_16_0_1_1449410509620_8892" class="" dir="ltr"><span
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
class=""><br>
</span></div>
<div id="yui_3_16_0_1_1449410509620_8892" class=""><span
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
class=""><br>
</span></div>
<div id="yui_3_16_0_1_1449410509620_8892" class=""><span
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
id="yui_3_16_0_1_1449410509620_8894" class="">Hi Ezequiel,</span><br
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
id="yui_3_16_0_1_1449410509620_8896" class="" clear="none">
<br style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;" id="yui_3_16_0_1_1449410509620_8898" class=""
clear="none">
<span style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;" id="yui_3_16_0_1_1449410509620_8900" class="">deviations
are not unexpected in general but not that large as you
report, so I wonder what's going on.. Could you please send
me input data and model files, as well as any ligand files
you used. If you customized some parameters, telling what
were those would be helpful too.</span><br
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
id="yui_3_16_0_1_1449410509620_8902" class="" clear="none">
<br style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;" id="yui_3_16_0_1_1449410509620_8904" class=""
clear="none">
<span style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;" id="yui_3_16_0_1_1449410509620_8906" class="">Please
send all files off-list to my email directly.</span><br
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
id="yui_3_16_0_1_1449410509620_8908" class="" clear="none">
<br style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;" id="yui_3_16_0_1_1449410509620_8910" class=""
clear="none">
<span style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;" id="yui_3_16_0_1_1449410509620_8912" class="">Thanks,</span><br
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
id="yui_3_16_0_1_1449410509620_8914" class="" clear="none">
<span style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;" id="yui_3_16_0_1_1449410509620_8916" class="">Pavel</span><br
style="font-family: 'Helvetica Neue', 'Segoe UI', Helvetica,
Arial, 'Lucida Grande', sans-serif; font-size: 13px;"
id="yui_3_16_0_1_1449410509620_8918" class="" clear="none">
<br style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;" id="yui_3_16_0_1_1449410509620_8920" class=""
clear="none">
</div>
<div class="" title="Ocultar el mensaje original"
role="presentation" id="yui_3_16_0_1_1449410509620_8110"
title-off="" style="font-family: 'Helvetica Neue', 'Segoe UI',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
13px;"><br>
<span class="" role="presentation" data-action="quoted-text"
id="yui_3_16_0_1_1449410509620_8112"></span></div>
<div class="" role="gridcell" tabindex="0"
id="yui_3_16_0_1_1449410509620_8129" style="transition: none;
font-family: 'Helvetica Neue', 'Segoe UI', Helvetica, Arial,
'Lucida Grande', sans-serif; font-size: 13px;">
<blockquote type="cite" id="yui_3_16_0_1_1449410509620_8136"
class="">
<div id="yui_3_16_0_1_1449410509620_8135"
style="font-family: HelveticaNeue, 'Helvetica Neue',
Helvetica, Arial, 'Lucida Grande', sans-serif; font-size:
16px;" class="">
<div id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class="">Hello, I'm working in a refinement that I
started some time ago. I noted that repeating the same
refinement task using a newer version of phenix, the
refinement statistics Before and After refinement are
different from values of the old version (I used
"restore job" from the Job history to repeat the same
task in the two versions installed in the same PC). Any
explanation? I'm worried about the rms deviation. Thanks
in advance.</div>
<div dir="ltr"
id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class=""><br id="yui_3_16_0_1_1449410509620_8933"
class="" clear="none">
</div>
<div dir="ltr"
id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class="">new version:</div>
<div id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class="">R-work: start=0.1697, final=0.1761</div>
<div id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class="">R-free: start=0.2011, final=0.2053</div>
<div id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class="">Bonds: start=0.046, final=0.029</div>
<div id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class="">Angles: start=1.321, final= 0.631</div>
<div id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class=""><br id="yui_3_16_0_1_1449410509620_8941"
class="" clear="none">
</div>
<div dir="ltr"
id="yiv1589213489yui_3_16_0_1_1449410509620_4803"
class="">old version:</div>
<div class=""
id="yiv1589213489yui_3_16_0_1_1449410509620_4803">R-work:
start=0.1651, final=0.1657</div>
<div class=""
id="yiv1589213489yui_3_16_0_1_1449410509620_4803">R-free:
start=0.2018, final=0.2009</div>
<div class=""
id="yiv1589213489yui_3_16_0_1_1449410509620_4803">Bonds:
start=0.013, final=0.013</div>
<div class="" dir="ltr"
id="yiv1589213489yui_3_16_0_1_1449410509620_4803">Angles:
start=1.409, final= 1.411</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
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