[phenixbb] message after refinement

Pavel Afonine pafonine at lbl.gov
Tue Jul 14 10:15:46 PDT 2015

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?


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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