I am running phenix.refine (version 2008_05_03_2330) with the command-line options ordered_solvent=true ordered_solvent.mode=filter_only During the final step (3_bss), my R and Rfree increase significantly. Any thoughts on why this jump would occcur? Per the notations in the logfile, only 30 waters were removed in the final model. Thanks, Jennifer R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.1564 0.1709 2.905699e+00 3.076326e+00 1_bss: 0.1145 0.1431 2.837441e+00 3.027552e+00 1_xyz: 0.1159 0.1433 2.846219e+00 3.029651e+00 1_adp: 0.1159 0.1433 2.846219e+00 3.029651e+00 1_occ: 0.1155 0.1429 2.844726e+00 3.028603e+00 2_bss: 0.1154 0.1427 2.844702e+00 3.028393e+00 2_xyz: 0.1151 0.1427 2.842538e+00 3.027628e+00 2_adp: 0.1151 0.1427 2.842538e+00 3.027628e+00 2_occ: 0.1151 0.1427 2.842433e+00 3.027654e+00 3_bss: 0.1151 0.1426 2.842430e+00 3.027578e+00 3_xyz: 0.1156 0.1428 2.846107e+00 3.029162e+00 3_adp: 0.1156 0.1428 2.846106e+00 3.029160e+00 3_occ: 0.1156 0.1429 2.846122e+00 3.029225e+00 3_bss: 0.1306 0.1512 2.943092e+00 3.079441e+00