Hi Joel,

What is the command to report the average ADP for protein main chain and side chains (Similar to the CNS model_stats function)? Is there also an easy command to report average ADP of protein, solvent and ligands separately? 

phenix.model_vs_data model.pdb data.mtz

More information:

J. Appl. Cryst. (2010). 43, 669-676
phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics
P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart and P. D. Adams

You probably need to use a recent version of PHENIX.

Pavel.