A depiction of the conformations of the second copy of the ligand from PDB entry 1ive. (a), (b) and (c) show the deposited (C atoms colored green), AFITT–CIF (C atoms coloured red) and PHENIX–AFITT (C atoms colored turquoise) conformations, respectively. The density shown is σA-weighted 2Fo − Fc density contoured at 1σ and the difference map was contoured at 3σ. (d) shows the deposited and PHENIX–AFITT conformations using the previously described color scheme, where the r.ms.d. is 0.81 Å and the energy difference is 134 kJ mol−1. (e) shows an overlay of the AFITT–CIF and PHENIX–AFITT conformations. The r.m.s.d. is 0.31 Å and the energy difference is 41.6 kJ mol−1. There are no examples in this data set where the r.m.s.d. between the AFITT–CIF and PHENIX–AFITT conformations exceeds 0.4 Å, yet the energy difference between the two conformations was almost always large (>10 kJ mol−1).