Hi Pan,

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.

I would appreciate if you tell us what you find.

If you are using the command line then it is

phenix.real_space_refine model.pdb map.ccp4 resolution=3.1 nonbonded_weight=10000

In the GUI:
Refinement Settings -> All parameters -> Search parameters : type into prompt nonbonded_weight, then OK -> In pop up prompt change 1000 to a desired value.

Pavel

On 11/22/17 17:19, 潘晓伟 wrote:

Hello everyone

I refine a cryo EM data with 3.1 angstrom, the model fit well with the map, but the clashscore is high, abot 23.

How can I decrease the value of clashscore with realspace.refinement in Phenix GUI.

Thanks!

Pan