. 2016 Sep 26;5:e17219. doi: 10.7554/eLife.17219

Table 2.

Comparison of structure refinement results between Rosetta and phenix.real_space_refine*.

DOI: http://dx.doi.org/10.7554/eLife.17219.017

	RSCC*^,†,‡ validation map	iFSC*^,†,§ validation map	EMRinger Score*^,† validation map	MolProbity^†				Number of residues with better RSCC^†,¶
	RSCC*^,†,‡ validation map	iFSC*^,†,§ validation map	EMRinger Score*^,† validation map	Score	Clash score	Rotamer outliers [%]	Ramachandran favored [%]	Number of residues with better RSCC^†,¶
TRPV1	0.785 / 0.790	0.546 / 0.566	1.84 / 1.90	1.59 / 1.48	4.30 / 2.14	0.00 / 0.00	94.41 / 91.72	86 / 250
Frh	0.835 / 0.835	0.504 / 0.517	1.36 / 1.27	1.68 / 1.62	7.99 / 3.66	0.68 / 0.13	96.31 / 92.67	677 / 1328
Mitoribosome	0.832 / 0.832	0.476 / 0.478	2.05 / 1.98	1.88 / 1.62	6.17 / 4.08	0.38 / 0.00	90.19 / 93.49	415 / 564

*To avoid over-fitting, refinement using both methods was carried out using the half-map approach, in which the models were subject to refinement using the training maps. The results showing here were evaluated using the validation-maps. The input model information is the same as reported at Table 1.

^†Numbers (scores) from phenix.real_space_refine (left) versus (/) Rosetta refined (right) model.

^‡Real-space correlation coefficients were evaluated using UCSF Chimera.

^§Integrated Fourier shell correlation (iFSC) from 10–3.4Å resolution shells.

^¶We calculate per-residue real-space correlation coefficient and report the number of residues which show the value of ΔRSCC greater than 0.05.