[phenixbb] Rfree increases during ordered solvent filtering

[Jennifer L Ekstrom]

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 
>> 
>