Hi Jennifer, you are using "ordered_solvent.mode=filter_only". This means that the new waters are not added but the existing ones are filtered (removed) at final step based on selection criteria (B-factors, distances, H-bonding, etc...). Do you really want this? If not, then do not use "ordered_solvent.mode=filter_only" (the default is "auto" which is good in most of cases). Please let me know if you have any questions! Pavel. On 6/24/2008 2:42 PM, Jennifer L Ekstrom wrote:
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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb