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: http://phenix-online.org/presentations/nb_weight.pdf Hope this answers your question! Get back to us if not. Pavel