The first two stages of electron-density interpretation in the phasing of the molecular-replacement case. (a), (b), (c) and (d) show the first stage of model building. The electron-density maps shown in (a), (b), (c) and (e) are only displayed in areas that are not occupied by cathepsin V molecules. In (a), (b) and (c) the 2Fobs − Fmodel maximum-likelihood weighted map, the real-space averaged map from (a) and the score-averaged map from (b) rendered using a 2.2 Å sphere are shown, respectively. In (d) the molecular model (shown in green) built using these maps is shown on the background of the chain trace of the final structure of clitocypin. (e) and (f) show the second stage of model building. In (e), which is equivalent to (c), the score map of averaged density is shown. (f) is equivalent to (d); the difference is that here the molecular model at the end of the second stage is shown. POV-Ray was used to render the images.