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