Hi Enrico,
However, I would be very grateful if someone could point me to the topic already posted in the message below by Dr. Scott few days ago, exactly at: "a quick description for depositing phenix-refined coordinates?", though the full message contained very interesting points I would love to hear about
We don't have a dedicated deposition tool yet, sorry. But we are actively working with the PDB on this. In the meantime, the .pdb files produced by phenix.refine are the best starting point.
(I also performed refinement by refmac/phenix, and observed kind of a similar trend for those numbers).
It may be because we are reporting mean deviations instead of root-mean-square deviations. This is kind of an oversight on our part and will be changed in the next version. Ralf