[phenixbb] message after refinement

Almudena Ponce Salvatierra maps.farma at gmail.com
Tue Jul 14 04:56:24 PDT 2015

Dear all,

after refinement of my nucleic acid structure with phenix.refine I get:
"warning: rms deviation from ideal geometry (bonds and/or angles) is
suspisciously high. You may need to optimize X-ray stereochemistry

However when I move to the molprobity tab I see no outliers no anything...
looking weird.

I even more wonder where this comes from because the fact is that I had one
refinement with no warnings or anything and today I repeated the same,
exactly the same, except for the fact that I renumbered one of the chains.
Now all out of a sudden (I know it doesn't sound scientific at all), I get
this warning regarding the rmsd when I was actually considering that the
refinement stage was over.

Does anybody have a theory regarding where the problem might be here?

Thanks a lot in advance.

Best wishes,


Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
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