1. A method for improving an electron density map representing a crystal structure comprising: (a) obtaining by x-ray diffraction observed structure factor amplitudes for a plurality of reflections from the crystal structure; (b) selecting a starting set of crystallographic phases to combine with the observed structure factor amplitudes to form a first set of structure factors; (c) deriving a first electron density map from the first set of structure factors; (d) identifying features of the first electron density map to obtain expected distributions of electron density; (e) making a comparison between the first electron density map and the expected distribution of electron density; (f) estimating how changes in the crystallographic phase of a reflection k affect the comparison; (g) establishing crystallographic phase probability distributions from the comparisons for the possible crystallographic phases of reflection k; (h) repeating steps (c) through (g) as k is indexed through all of the plurality of reflections; (i) deriving an updated electron density map using crystallographic phases determined to be most probable from the crystallographic phase probability distributions for each one of the reflections; and (j) repeating steps (d) through (i) to obtain a final set of crystallographic phases with minimum bias from known electron density maps.