[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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