Phenix has its own way to do it which is "Comprehensive validation" available from the GUI. This includes validation of model, data and model-to-data fit. It is data-specific: there is one for crystallography (X-ray or neutron) and one for Cryo-EM. For best results, you need the latest version from nightly builds. Hope "wwpdb validation pipeline" is something along the same lines, or close at least.