[phenixbb] rotamer outlier and clash socre

Pavel Afonine pafonine at lbl.gov
Sun Feb 14 09:54:13 PST 2021

Hello Pan,

I refined a cryo-EM data with 3.2 angstrom, the model fit well with the 
map, but the rotamer outlier is too high, about 8%.  How can I decrease 
the value of rotamer outlier by realspace.refinement in Phenix GUI, and 
no need to adjust the residues one by one in Coot?

if you used latest version of Phenix, which is dev-4146 as of today:


then this is not expected, because phenix.real_space_refine has built-in 
ability to detect which residues need a fix and does an exhaustive 
grid-search in chi-torsion angle space to optimize it against the map 
and local environment.

If this happened using the latest version of Phenix, then this is an 
indication to me that something has gone wrong and we need to 
investigate. For this I'm asking to send all input files.

Residues that phenix.real_space_refine was unable to fix for whatever 
reason are best to fit manually in Coot.

And I can't agree more with Tristan -- all the great tools and 
automation are to help you not substitute you! So, checking manually is 

Another question is the value of clash score are also too high.

You did not tell us the value, so no answer here!
A general guidance: the lower the better, but zero is not the goal.

When I set the nonbonded_weight to 10000

According to study we conducted recently:


this unlikely to be a great idea.


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