A depiction of the conformations of the first copy of the ligand from PDB entry 4cox. (a), (b) and (c) show the deposited (C atoms colored green), AFITT–CIF (C atoms colored red) and PHENIX–AFITT (C atoms colored turquoise) conformations, respectively. The density shown is σA-weighted 2Fo − Fc density contoured at 1σ. No difference density was observed when the density was contoured at 3σ. There are a total of four copies of the ligand in this deposition. (d) and (e) show the overlay for the first copy between the deposited and AFITT–CIF and between the AFITT–CIF and PHENIX–AFITT conformations, respectively, using the previously described coloring scheme. The r.m.s.d. between the deposited and the AFITT–CIF conformation was 0.24 Å, whereas the difference between the AFITT–CIF and PHENIX–AFITT conformations was 0.38 Å. In this case the AFITT–CIF refinement was unable to find the low-energy conformation generated by the PHENIX–AFITT refinement, as shown by the r.m.s.d. and the difference energies of 1.57 kJ mol−1 for the deposited versus AFITT–CIF and 119 kJ mol−1 for the deposited versus PHENIX–AFITT conformation. (f, g) Copy 4 presents a different result. The AFITT–CIF and PHENIX–AFITT methods both find a lower energy conformation where the r.m.s.d. for the deposited versus AFITT–CIF and deposited versus PHENIX–AFITT was 0.7 Å, but the r.m.s.d. for the AFITT–CIF and PHENIX–AFITT conformations was only 0.20 Å. The energy differences were 31.2 kJ mol−1 for deposited versus AFITT–CIF and 117 kJ mol−1 for deposited versus PHENIX–AFITT. An interesting observation from this example is that the PHENIX–AFITT method appears to be more consistent at finding low-energy conformations (the standard deviation across the four samples was 4.08 kJ mol−1), whereas the AFITT–CIF method was not as consistent (standard deviation of 19.6 kJ mol−1).