[phenixbb] modelvsdata output ksol and bsol are 0

[Pavel Afonine]

  Hi Hailiang,

I guess the only way to find out is to talk to the authors of that 
structure hoping that they may to explain what happened to the data: why 
a structure with reported ~70% solvent content has refined ksol=0 ( = no 
solvent evidence in the data).

Pavel.


  On 3/19/11 6:36 PM, zhangh1 at umbc.edu wrote:
> Thanks Pavel! My phenix (1.6.4-486) generated the same R/Rfree as you
> have, but just ended up with all 0 ksol and bsol. Just very weird. Thanks
> anyway.
>
> Hailiang
>
>>    Hi Hailiang,
>>
>> this is what one of my slides on validation is about (see page 29):
>> http://www.phenix-online.org/presentations/latest/pavel_validation.pdf
>>
>> I just ran phenix.model_vs_data on this PDB entry and I wonder what it
>> took to deposit it at all, given:
>>
>> - this poor geometry counts:
>>
>>       Molprobity statistics:
>>         Ramachandran plot, number of:
>>           outliers : 30    (10.14 %)
>>           allowed  : 58    (19.59 %)
>>           favored  : 208   (70.27 %)
>>         Rotamer outliers        : 61 (22.43 %)
>>
>> - such a suspicious Rfree-Rwork gap, most likely indicating
>> under-refinement:
>>
>>     Model_vs_Data:
>>       r_work(re-computed)                : 0.3479
>>       r_free(re-computed)                : 0.3590
>>       bulk_solvent_(k_sol,b_sol)         : 0.09  306.62
>>
>> although what's nice it is reproducible:
>>
>>     Information extracted from PDB file header:
>>       program_name    : REFMAC
>>       year            : 9
>>       r_work          : 0.346
>>       r_free          : 0.354
>>
>> Yes, one may naively like such a small rfree-rwork gap, but it's good to
>> realize that if you refine just one parameter per whole your structure,
>> say a scale factor between Fobs and Fcalc, then your Rfree will not be
>> much different compared to Rwork. It's all about proper parametrization
>> and achieving refinement convergence...
>>
>> Good luck!
>> Pavel.
>>
>>> Hi,
>>>
>>> I run phenix.modelvsdata on several systems and found from the output
>>> file
>>> that, the optimized ksol and bsol is 0. One example is the system of
>>> 3FUS.
>>> Any suggestions are appreicated!
>>>
>>> Best Regards, Hailiang
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>>
>
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