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Figure 5
Summary of the refinement results starting from the scrambled models. All data shown in these graphs are also tabulated in Supplementary Table S3. (a) Difference in Rfree values between the original PDB depositions and the structures obtained through Amber-based refinement of the S-models. The data are from 74 test-set structures where Rfree is reported as part of the PDB deposition (sorted in this plot according to the crystallographic resolution). A green color indicates that the Amber-refined structure is superior to the original PDB structure and a red color indicates that the Amber-refined structure is inferior to the original PDB structure. (b) MolProbity score percentiles for the structures obtained through Amber-based refinement of the S-models (semi-transparent green bars) and the original PDB structures (semi-transparent red bars). Of note, the MolProbity scores of the Amber-refined structures are somewhat adversely affected by the addition of ordered water (see Fig. 2[link]): before this step the average MolProbity score percentile is 86th, while after this step it drops to 76th. (c) Difference in Rfree values between the structures obtained through Phenix- and Amber-based refinement of the S-models. The data are from 84 test-set PDB entries. An exceedingly high ΔRfree of 0.139 (rightmost bar in the plot) reflects the failure of Phenix for this particular structure. (d) MolProbity score percentiles for the structures obtained through Amber- and Phenix-based refinement of the S-models.

IUCrJ
Volume 9| Part 1| January 2022| Pages 114-133
ISSN: 2052-2525
https://doi.org/10.1107/S2052252521011891