The mythical X-GEN paper in J. Appl. Cryst. still hasn't been
written, and until it is, the following is probably the best reference
for the software:
Howard, Andrew J. (2000) Data processing in macromolecular crystallography. Chapter in: Crystallographic Computing 7: Proceedings from the Macromolecular Crystallographic Computing School, 1996. P.E. Bourne and K.D. Watenpaugh, eds. Oxford: Oxford University Press.