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Typically, if clashes don't get resolved automatically it means bits
of model where clashes occur are trapped in local minima that cannot
be escaped by gradient-driven minimization. Try SA refinement or fix
manually, then re-run your usual refinement.<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 9/27/15 18:21, Smith Lee wrote:<br>
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cite="mid:615863586.1820571.1443403281522.JavaMail.yahoo@mail.yahoo.com"
type="cite">
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<div id="yui_3_16_0_1_1443402861073_2532"> Dear All,</div>
<div id="yui_3_16_0_1_1443402861073_2533"><br>
</div>
<div id="yui_3_16_0_1_1443402861073_2501">With the EM cryo data,
I have compared the function of phenix.real_space_refine of
Phenix10 and Phenix1.9-1692. For the Ramachandran favored, the
new version is about 90%, the old version is about 92%. For
the clashscore by Molprobity, the new version is about 30, the
old version is about 20. Molprobity indicated the clashing
atoms were systematically existing in the whole molecule,
rather than on specific parts of the protein which may be
indication of bad modelling.</div>
<div id="yui_3_16_0_1_1443402861073_2692"><br>
</div>
<div id="yui_3_16_0_1_1443402861073_2691">Clearly the clashscore
of 30 is unacceptable. Will you please give some advise on how
to improve the function of new version of Phenix, considering
adding H was not suitable as for the resolution was poorer
than 4.0 A?</div>
<div id="yui_3_16_0_1_1443402861073_2739"><br>
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<div>Smith</div>
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