Direct-space methods in phase extension and phase determination. II. Developments of low-density elimination

The low-density elimination method for phase extension and refinement [Shiono & Woolfson (1992). Acta Cryst. A48, 451-456] has been improved by substituting a smoother density-modification procedure for the original sharp cut-off function. In addition, better criteria have been found for limiting the number of refinement cycles, which gives a better final result for much less work. The effectiveness of the process has been illustrated by phase refinement for a protein with high-resolution (1.17 Å) data containing 808 independent non-H atoms plus 83 water molecules in the asymmetric unit; the unweighted mean-phase error was reduced from 74 to 39.3°. Phase extension and refinement was also demonstrated for pig 2Zn insulin starting with multiple isomorphous replacement (MIR) phases at 1.9 Å and extending out to 1.5 Å. There was a significant improvement of phases and the final map had a correlation coefficient of 0.540.