Hi Smith, No, the output of cut_out_density is FWT PHWT and is not interpretable by phenix.refine which requires F,SIGMA. You may find it easier to use phenix.real_space_refine for this purpose! If you really want to refine with phenix.refine (make sure you understand all the implications of doing this!) you can extract FWT and call it FP and add SIGFP=1 with: phenix.resolve --giant<http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]