Since multiple symmetry operators exist in real space it is possible that the two sites relate to a different origin. These solutions correspond to the four possible origin choices in this example and the correct choice can be determined by looking for cross peaks at the proper location between this site and site 1. Each of these programs will refine heavy atom coordinates, occupancies and, if desired, temperature factors. Several cycles of refinement can be done with periodic recalculation of the phases. Phase refinement has been successfully used to solve structures for decades but can be tricky with irritating instabilities and weighting problems.
Some authorities prefer maximum likelihood refinement which is thought to be more stable.
In our example we will perform 6 cycles of refinement with 2 recalculations of the phases. We will be doing traditional phase refinement. The parameters change very little during refinement which suggests that the locations of our sites are close to being correct. Otherwise it is run just as before. In this example, set the contour levels at one sigma and start contouring at two sigma.