Table 1. Validation scores for original, re-refined and manually optimized structure models.

PDB code	1lf2	1zcs	2ete	2qc1	2vno
Resolution (Å)	1.80	1.45	1.75	1.94	1.45
R (%)
Original†	24.0 (19.5)	18.0 (15.8)	18.2 (18.1)	22.7 (21.4)	19.5 (18.0)
Re-refined	17.6	17.3	15.9	19.2	19.5
Manually optimized	17.4	15.2	14.8	18.6	18.7
Rfree (%)
Original†	27.8 (25.8)	19.8 (18.0)	18.3 (19.4)	24.8 (23.3)	24.1 (22.6)
Re-refined	22.2	19.5	17.9	23.9	24.1
Manually optimized	21.3	17.3	16.6	23.4	22.0
Non-water atoms
Original	2658	6955	3020	2426	2753
Re-refined	2644	6955	3020	2426	2753
Manually optimized	2663	6981	3057	2434	2781
Waters
Original	338	1002	308	187	574
Re-refined	338	1002	308	187	574
Manually optimized	254	1005	378	193	532
Atomic overlaps‡
Original	59	72	23	145	58
Re-refined	64	72	31	143	58
Manually optimized	53	87	23	87	42
Packing quality§
Original	−1.94	−1.51	−1.97	−1.87	−2.38
Re-refined	−1.96	−1.53	−1.98	−1.79	−2.38
Manually optimized	−1.83	−1.50	−1.97	−1.79	−2.30
Ramachandran§
Original	−1.86	0.07	0.05	−0.62	0.24
Re-refined	−1.43	0.05	−0.23	−0.26	0.24
Manually optimized	−1.44	0.06	−0.16	−0.17	0.39
Rotamer normality§
Original	−2.38	0.51	0.26	−0.26	−0.11
Re-refined	−1.83	0.42	0.28	−0.37	−0.11
Manually optimized	−1.24	0.63	0.67	−0.39	0.28
Backbone conformation§
Original	−3.87	−1.90	−2.31	−1.44	−2.18
Re-refined	−3.61	−1.95	−2.56	−1.31	−2.18
Manually optimized	−3.37	−1.82	−2.57	−1.29	−2.04
Bond r.m.s.Z
Original	0.74	0.46	0.43	0.38	1.40
Re-refined	0.96	0.49	0.95	0.96	1.40
Manually optimized	0.61	0.40	0.80	0.70	0.60
Angle r.m.s.Z
Original	0.94	0.69	0.60	0.75	0.87
Re-refined	1.00	0.68	0.83	0.93	0.87
Manually optimized	0.80	0.65	0.76	0.81	0.87
Side-chain planarity r.m.s.Z
Original	0.83	0.59	0.38	0.26	2.01
Re-refined	1.23	0.66	1.04	1.15	2.01
Manually optimized	0.71	0.55	0.86	0.80	0.90

^†Calculated from experimental data; PDB header values are given in parentheses.

^‡van der Waals overlap greater than 0.40 Å.

^§ WHAT_CHECK Z scores.