Section 25.2.1.6.2.1. `Classical' phase refinement

With this option, one minimizes for isomorphous-replacement data or for anomalous-scattering data with respect to the desired parameters. Typically, the weights are taken as the reciprocal of the `standard error' (expected lack of closure) or its square. The summations are taken over all reflections for which the protein phase is thought to be reasonably valid, usually implied by a figure of merit of 0.4 or higher. The protein phase estimate usually comes from the centroid of the appropriate combined phase probability distribution given by equation (25.2.1.10); however, one has the option of including all data sets when combining the distributions, or including all except that for the derivative being refined. Once new heavy-atom and scaling parameters are obtained, new individual SIR or SAS phase probability distributions are computed and combined to provide new protein phases, and these phases are used to update the standard error estimates as described earlier. Then the individual distributions are recomputed once more using the new standard error estimates, and these distributions are combined again to give new protein phase estimates. The process is then iterated using the new phases and new heavy-atom parameters to start another round of refinement. After several iterations, the heavy-atom parameters, standard error estimates and protein phase estimates converge to their final values.