[phenixbb] Rfree increases during ordered solvent filtering

[Pavel Afonine]

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 
>>>
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>>
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