**Figure 1**
Map-likelihood phasing of initiation factor 5a. (*a*) Experimental (MAD) map. (*b*) Map-likelihood phased map, using experimental phases as a starting phase set. (*c*) Map-likelihood phased map, using maximum-likelihood density-modified phases as starting phase set. Experimental (MAD) phases for initiation factor 5a (Peat *et al.*, 1998) had an overall figure of merit of 0.61 to 2.2 Å. The refined model of initiation factor 5a (PDB entry 1bkb
; Berman *et al.*, 2000) is overlaid on the experimental map. The map is contoured at 1.5σ. In (*b*), one cycle of map-likelihood phasing was carried out and phase probabilities were calculated from the map likelihood only. The figure of merit of map-likelihood phases was 0.37. The calculation of the solvent mask and the map-likelihood phasing was carried out as described for maximum-likelihood density modification (Terwilliger, 2000), except that experimental phases were not used in the phase-probability calculation. Experimental phases were used in determining the mask, as in maximum-likelihood density modification. In (*c*), a full set of five mask cycles of maximum-likelihood density modification, each with ten minor cycles of phase improvement, were carried out. These phases were then used to calculate a mask and to initiate one cycle of map-likelihood phasing as in (*b*). The figure of merit of map-likelihood phasing was 0.50. |