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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