[phenixbb] real space refine and nonbonded_weight

Pavel Afonine pafonine at lbl.gov
Fri Oct 25 11:48:43 PDT 2019

Hi Alan,

> Dear Developers
> A structure we refined back in 2017, using phenix.real_space_refine on 
> a cryoEM map @ 3.7A (version 1.11.1–2575) produces a clashscore of ~8 
> but the exact same refinement run with the latest phenix (version 
> 1.17.1) generates a clashscore of ~22.  Our refinements with the 
> latest version on other EM structures tend to generate pretty high 
> clashscores too.
> I think i've tracked this down to the nonbonded_weight parameter, 
> which defaults to 1000 in the older version, and to 100 in the latest 
> version.
> At which version did the default change, and is there a reason for 
> it?  I couldn't find it in the changelog.
> Alan

yes, we did change nonbonded_weight from 1000 to 100 at some point in 
the past. This was based on a quick investigation that I did, details 
are here:


Hope this answers your question! Get back to us if not.


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