density modification DENS_MOD averaging DENS_MOD DENS_MOD DENS_MOD rms_fit.cmds RMS_FIT rms RMS_FIT fit RMS_FIT superposition RMS_FIT RMS_FIT RMS_FIT make_masks.cmds MAK_MASK molecular mask MAK_MASK mask MAK_MASK envelope MAK_MASK MAK_MASK MAK_MASK DM_PREP DM_PREP density modification initial map DM_PREP prepare DM_PREP DM_NEXT DM_NEXT density modification DM_NEXT cyclic averaging DM_NEXT averaging DM_NEXT