Hi,

Sorry for the late reply.

First, please make sure you are using the latest Phenix version (currently 1.20.1). The error indicates that refinement became unstable for some reason.

Possible causes of this include:
- using NCS constraints which include only part of a chain.
- bad geometry in the starting model, like terrible clashes

Ways to overcome:
- Check NCS annotations, missing atoms/residues etc or disable NCS constraints,
- increase the value of parameter max_reasonable_bond_distance to e.g. 500.

Best regards,
Oleg Sobolev.

On Tue, Mar 15, 2022 at 3:36 PM Mullins, Elwood A. <elwood.mullins@vanderbilt.edu> wrote:
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.

Thanks,

Elwood


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