**Figure 2**
Effect of solvent content on map-likelihood phasing. Mean true figure of merit (〈cosΔφ〉) is plotted as a function of cycle number for simulations phased based on map likelihood with model cases having solvent contents of 31 (closed diamonds), 39 (open triangles), 47 (closed triangles), 53 (open squares), 59 (closed squares), 66 (open circles) and 73% (closed circles). Model phases were calculated from a model based on the refined structure of dehalogenase from *Rhodococcus* (Newman *et al.*, 1999; PDB entry 1bn7
), except that varying numbers of atoms were omitted from the calculation to simulate varying solvent content. The space group is *P*2_{1}2_{1}2, with unit-cell parameters 93.8, 79.8 and 43.1 Å, and the resolution limits used were from 20 to 2.8 Å. The protein atoms in the simulations in Fig. 2(*a*) occupy from 27 to 69% of the unit cell, based on an algorithm in which all points within 2.5 Å of an atom in the model are considered occupied by protein. In each simulation, a starting set of phases was generated by adding Gaussian errors to the model phases so as to achieve a mean true figure of merit (〈cosΔφ〉) of 0.32. This starting set of phases, along with model amplitudes, was used to initiate map-likelihood phasing. Solvent masks were based on the atomic models in this simulation. In (*a*), the mean true figure of merit (〈cosΔφ〉) is plotted as a function of cycle number for simulations with solvent content of 31 (closed diamonds), 43 (open triangles), 47 (closed triangles), 53 (open squares), 59 (closed squares), 66 (open circles) and 73% (closed circles). In (*b*), the simulation with 53% solvent was repeated using varying high-resolution cutoffs (open circles) or low-resolution cutoff (closed circles) and the final mean true figure of merit after 20 cycles is plotted. |