Difference map features produced by simulated-annealing refinement against ligand-free native structures clearly reveal ligand binding and active-site rearrangements in the absence of the risk of model bias. Fo − Fc OMIT maps, contoured at 3σ, are shown for DCP data subsets refined versus the native DHP structure. In each case, the native DHP structure from OMIT refinement versus a particular subset is shown in grey, while the superimposed structure of the ligand complex is shown in blue. Positive difference map features are shown in green, with negative features in red. Note that the flips of Phe21 and Phe60 to accommodate ligand binding, together with the ligand density itself, are very clearly defined in the data set obtained from all data and this is maintained in the 5000-image subset. Clear OMIT map features are apparent for Phe60 and DCP in data sets with as few as 400 images, while this was no longer the case in the 300-image subset.