Hi Paul,
However, you can generate a geo file directly from a model with this commandline:
phenix.pdb_interpretation your_model.pdb write_geo_files=True
This is probably the more useful option for your purposes.
For understanding clashes, I recommend running phenix.clashscore and using its dedicated and complete output. This will return a list of all the clashes, sorted in order of severity.
As to non-bonded interaction distances, I believe that they are close approaches between atoms that are not covalently bonded. As you can see from the histogram bins (1.87 - 2.42, 2.42 - 2.96, 2.96 - 3.51, 3.51 - 4.05, 4.05 - 4.60A), these distances do not necessarily indicate clashes, but instead cover a range of distances in the general vdW contact region. The distribution of this histogram gives a general sense of how well packed the model is.
Very close non-bonded interactions may register as clashes in Probe and/or may generate various error messages in Phenix depending on your options. For various reasons, there is not an exact mapping between close non-bonded interactions and clashes.
Hopefully someone with a better understanding of the nonbonded distances will be able to chime in with a better explanation.
Good luck,
-Christopher Williams
---Richardson Lab, Duke University