[phenixbb] modelvsdata output ksol and bsol are 0

[zhangh1 at umbc.edu]

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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