<div dir="ltr">Hi,<div><br></div><div>Sorry for the late reply.</div><div><br></div><div>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.</div><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Possible causes of this include:</div><div style="font-size:12.8px">- using NCS constraints which include only part of a chain.</div><div style="font-size:12.8px">- bad geometry in the starting model, like terrible clashes</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Ways to overcome:</div><div style="font-size:12.8px">- Check NCS annotations, missing atoms/residues etc or disable NCS constraints,</div><div style="font-size:12.8px">- increase the value of parameter max_reasonable_bond_distance to e.g. 500.</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Best regards,</div><div style="font-size:12.8px">Oleg Sobolev.</div></div></div></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Mar 15, 2022 at 3:36 PM Mullins, Elwood A. <<a href="mailto:elwood.mullins@vanderbilt.edu">elwood.mullins@vanderbilt.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">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.<br>
<br>
I ran validation on the model. There are no bond length outliers and only minor other issues.<br>
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Any help would be greatly appreciated.<br>
<br>
Thanks,<br>
<br>
Elwood<br>
<br>
<br>
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