Table 4. Whole data-set averages for model-quality metrics.

Metric	PDB entry	Re-refined model	Final model
R (%)	19.8†	18.3	18.4
Rfree (%)	24.0†	22.0	22.2
Ramachandran plot‡	−1.30	−0.66	−0.61
Side-chain rotamers‡	−1.21	−0.69	−0.24
Coarse packing‡	−0.24	−0.16	−0.12
Fine packing‡	−0.97	−0.85	−0.70
No. of atomic bumps	108	78	82
No. of unsatisfied hydrogen-bond donors/acceptors	43	37	37

^†Values extracted from the PDB header.

^‡Model-normality Z scores from WHAT_CHECK with respect to a test set of 500+ high-resolution structure models. Higher values are better.