[phenixbb] Rfree increases during ordered solvent filtering
Pavel Afonine
PAfonine at lbl.gov
Wed Jun 25 13:21:20 PDT 2008
Hi Jennifer,
yes, I see it now: there must be something weird indeed. At this point I
can't tell you much without playing with the refinement myself. Is it
possible that you send me the data and model (to my address, not to the
whole phenixbb) so I can reproduce this behavior and possibly fix it or
suggest how to proceed? I promise to keep the files strictly
confidential and remove them from my computer once the issue is fixed.
Pavel.
On 6/25/2008 1:05 PM, Jennifer L Ekstrom wrote:
> Hi Pavel,
> Thanks. I don't believe that is the cause of this refinement
> anomaly. If I run the same job without the filter_only option, I am
> still seeing a very large jump in R/Rfree at the ordered solvent
> location/analysis/update step (before 2_xyz).
> ordered_solvent=true
> 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: 0.1313 0.1555 2.950732e+00 3.111378e+00
> 2_adp: 0.1307 0.1543 2.945031e+00 3.101981e+00
> 2_occ: 0.1306 0.1542 2.945015e+00 3.101954e+00
> 3_bss: 0.1301 0.1538 2.944930e+00 3.101580e+00
> 3_xyz: 0.1312 0.1565 2.951306e+00 3.117549e+00
> 3_adp: 0.1306 0.1546 2.940355e+00 3.100448e+00
> 3_occ: 0.1305 0.1546 2.940347e+00 3.100439e+00
> 3_bss: 0.1292 0.1534 2.940856e+00 3.100060e+00
> However, if I run this job with no ordered solvent manipulation, the
> R/Rfree are stable at their previous lower value.
> ordered_solvent=false
> 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: 0.1156 0.1429 2.846122e+00 3.029225e+00
>
> I wouldn't expect to see a 1% jump in Rfree after minor tweaking of a
> few dozen waters. This is not a small structure. There must be
> something strange in the refinement protocol during the ordered water
> treatment. I had thought it could be a weighting issue, but
> subsequent refinement with optimization of wxc and wxu does not bring
> the R/Rfree down to the original range.
> Thanks, Jennifer
> (Running version 2008_05_03_2330)
> ...................................................
>
>
> Pavel Afonine writes:
>> 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
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>
>
>
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