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<div class="moz-cite-prefix">On 10/24/16 23:50, Pavel Afonine wrote:<br>
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I think "weight=1" may be a troublemaker.. It may be too far from
what's optimal (that program determines by default if you don't
specify any weight) and that may result in clashes that happen
during refinement. Of course, something else may cause this as
well.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 10/24/16 20:07, Oleg Sobolev
wrote:<br>
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<div dir="ltr">Hi Julia,
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<div>In addition to Dorothee's response to your another
e-mail, I would indeed recommend check the model geometry,
in particular, bad atomic clashes (where 2 atoms are very
close to each other). You can find them in the .geo file
which should be created by this point or in log, under
"Nonbonded interactions:". The worst clashes will be the
first in the list.</div>
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<div>Best regards,</div>
<div>Oleg Sobolev.</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Oct 24, 2016 at 3:19 AM,
Flis, Julia <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:julia.flis@charite.de" target="_blank">julia.flis@charite.de</a>></span>
wrote:<br>
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<div
style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Hello,<br>
<br>
my question is about the Phenix real space
refinement. I am using the Phenix version
phenix-1.11-2563.<br>
<br>
My command looks as follows:<br>
phenix.real_space_refine <font color="#000000"><font
face="Tahoma"><font size="2">secondary_structure.enable=<wbr>true</font></font></font>
Model.pdb VOL.map elbow.Model_pdb.001.cif
Model.pdb_ss.eff resolution=3.8 weight=1<br>
<br>
My problem is that the refinement suddenly stops
during the first refinement cycle:<br>
<br>
<br>
<br>
Model_real_space_refined.log says:<br>
<br>
********************** REFINEMENT MACRO_CYCLE 1 OF
5 *************************<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Update NCS operators<br>
********************<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Update rotamer restraints<br>
*************************<br>
------------------------------<wbr>------------------------------<wbr>-------------------<br>
Global refinement<br>
*****************<br>
END<br>
<br>
<br>
In the shell I get this :<br>
<br>
[...]<br>
distance: 184426 - 184921: 3.388<br>
distance: 184428 - 184920: 3.342<br>
distance: 184448 - 184898: 3.373<br>
distance: 184449 - 184897: 3.187<br>
distance: 184491 - 184860: 3.066<br>
distance: 184531 - 184770: 3.203<br>
distance: 184554 - 184746: 3.137<br>
<br>
then it stops and the only files generated are
Model_real_space_refined.log and
Model_initial.geo.<br>
<br>
Could you give me an advise? I have no clue what
the problem could be.<br>
<br>
Thank you,<br>
<br>
Julia<br>
<br>
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