Ligand conformational energies from PDB-deposited models, AFITT–CIF refinement and PHENIX–AFITT refinement. (a, b, c) Histograms for PHENIX–AFITT (a), AFITT–CIF (b) and PDB-deposited (c) energies with kernel density estimates (KDE) of the distributions for the full set of test ligand energies. Means of each set of ligand conformation energies are shown in the legend. (d) A scatter plot comparing the conformation energy of each ligand obtained from a PHENIX–AFITT refinement against either the deposited PDB model (blue dots) or the models after refinement with an MMFF-derived CIF dictionary file (red dots). The mean percentage reduction in energy from using the PHENIX–AFITT protocol is 34% versus the PDB conformations and 22% versus AFITT–CIF.