[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):

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 

     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!

> 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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