[phenixbb] Error from exceeding max reasonable bond distance

Mullins, Elwood A. elwood.mullins at vanderbilt.edu
Tue Mar 15 15:32:02 PDT 2022

I’m having an issue with a real-space refinement job crashing after giving the following error: "RuntimeError : Bond distance > max_reasonable_bond_distance: 62.8014 > 50". I found mention of this problem in a post from 2017. I tried the recommended solution (setting the max reasonable bond distance to 999), but that caused the job to hang. I also tried clicking “proceed with excessive length bonds”. That didn’t make a difference; I received the same error message.

I ran validation on the model. There are no bond length outliers and only minor other issues.

Any help would be greatly appreciated.



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