Hi Almudena, what these values are? Could you please send me (off mailing list) model and data files after refinement for which you got this message? Thanks, Pavel On 7/14/15 04:56, Almudena Ponce Salvatierra wrote:

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 weighting"

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

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

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