[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?

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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