[phenixbb] Rfree increases during ordered solvent filtering
Pavel Afonine
pafonine at lbl.gov
Tue Jun 24 19:22:31 PDT 2008
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
>
>
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