Table 4. Comparison between reference-model restraints and DEN refinement.

Numbers in bold highlight values where the reference-model refinements are an improvement over DEN refinement. Bold PDB codes are models where reference-model restraints improved R _free, R _free R _work and Ramachandran score over the comparable DEN refinement. Individual bold values for R _free, R _free R _work and Ramachandran score are values that are an improvement over the equivalent value in DEN refinement.

		R free			R free R work			Ramachandran score
PDB entry	Resolution ()	PHENIX	PHENIX with reference	DEN†	PHENIX	PHENIX with reference	DEN†	PHENIX	PHENIX with reference	DEN†
1av1 ‡	4.00	0.343	0.342	0.335	0.11	0.08	0.07	0.462	0.898	0.840
1jl4	4.30	0.344	0.320	0.353	0.11	0.08	0.12	0.655	0.803	0.718
1r5u	4.50	0.248	0.245	0.334	0.05	0.04	0.05	0.627	0.896	0.714
1xdv	4.10	0.345	0.348	0.358	0.11	0.11	0.12	0.758	0.833	0.780
1xxi	4.10	0.297	0.278	0.407	0.09	0.06	0.05	0.538	0.958	0.842
1ye1	4.50	0.318	0.289	0.312	0.16	0.12	0.08	0.818	0.975	0.894
1yi5	4.20	0.317	0.284	0.323	0.10	0.06	0.07	0.608	0.944	0.758
1z9j	4.50	0.236	0.229	0.317	0.08	0.07	0.07	0.593	0.952	0.838
2a62	4.50	0.371	0.354	0.340	0.14	0.11	0.07	0.629	0.749	0.590
2bf1 ‡	4.00	0.421	0.432	0.479	0.07	0.05	0.12	0.480	0.666	0.467
2i36	4.10	0.412	0.403	0.387	0.09	0.06	0.02	0.568	0.889	0.839
2qag	4.00	0.378	0.379	0.392	0.04	0.04	0.02	0.471	0.781	0.616
2vkz ‡	4.00	0.278	0.272	0.327	0.08	0.07	0.05	0.770	0.969	0.832
3bbw	4.00	0.321	0.305	0.304	0.08	0.05	0.01	0.806	0.942	0.876
3crw	4.00	0.339	0.292	0.324	0.10	0.06	0.09	0.781	0.872	0.836
3dmk	4.19	0.292	0.282	0.407	0.12	0.09	0.08	0.707	0.827	0.742
3du7	4.10	0.304	0.302	0.332	0.10	0.07	0.09	0.553	0.838	0.730
Average	4.18	0.327	0.315	0.355	0.096	0.072	0.069	0.637	0.870	0.760

^†Data taken from Table 2 in Schrder et al. (2010 ▶).

^‡ 1av1, 2bf1 and 2vkz were included in the DEN test set as controls where the reference homology model has an 10 r.m.s.d. difference from the starting model.