[phenixbb] modelvsdata output ksol and bsol are 0
Pavel Afonine
pafonine at lbl.gov
Sat Mar 19 00:23:04 PDT 2011
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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