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Hi Pan,<br>
<br>
first off I suggest to inspect top worst clashes and see if they can
be addressed. If that does not help, then try running several
refinement runs each one using "nonbonded_weight" set to say 1000
(the default value), 5000, 10000, 25000, 50000. See how that changes
the clashscore and model-to-map fit.<br>
<br>
I would appreciate if you tell us what you find.<br>
<br>
If you are using the command line then it is<br>
<br>
phenix.real_space_refine model.pdb map.ccp4 resolution=3.1
nonbonded_weight=10000<br>
<br>
In the GUI:<br>
Refinement Settings -> All parameters -> Search parameters :
type into prompt nonbonded_weight, then OK -> In pop up prompt
change 1000 to a desired value.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 11/22/17 17:19, 潘 晓伟 wrote:<br>
</div>
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<div>Hello everyone</div>
<div> </div>
<div>I refine a cryo EM data with 3.1 angstrom, the model fit well
with the map, but the clashscore is high, abot 23.</div>
<div> </div>
<div>How can I decrease the value of clashscore with
realspace.refinement in Phenix GUI.</div>
<div> </div>
<div>Thanks!</div>
<div> </div>
<div>Pan<br>
</div>
</blockquote>
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