. 2013 May 16;41(Web Server issue):W256–W265. doi: 10.1093/nar/gkt403

Table 1.

Logistic regression classifiers’ coefficient estimates and standard errors

Descriptor	First-stage classifier	Second-stage classifier
	Coefficient (standard error)	n_T	Coefficient (standard error)
Intercept	−12.19 (1.31)^a	all	−5.62 (1.20)^a
1. Fraction residues correctly placed. (fixed distance threshold of 0.5 Å)	−6.27 (1.35)^a	3	1.62 (0.55)^b
	−6.27 (1.35)^a	4+	−1.33 (1.42)
2. Fraction residues correctly placed (relative distance threshold of 10%)	5.39 (2.36)^c
3. Residue-pair distance difference	0.83 (0.44)^d	3	−0.25 (0.13)^d
3. Residue-pair distance difference	0.83 (0.44)^d	4+	−0.82 (0.23)^a
4. Normalized residue-pair distance difference	1.40 (0.36)^a	3	−0.24 (0.21)
4. Normalized residue-pair distance difference	1.40 (0.36)^a	4+	0.20 (0.26)
5. Position of backbone atoms		3	0.96 (0.17)^a
5. Position of backbone atoms		4+	1.14 (0.29)^a
6. Orientation of backbone atoms		3	0.45 (0.12)^a
6. Orientation of backbone atoms		4+	0.80 (0.16)^a

^aSignificant at 0.1% level.

^bSignificant at 1% level.

^cSignficant at 5% level.

^dSignificant at 10% level.

The first-stage and second-stage classifiers use different subsets of descriptors; the second-stage classifier distinguishes between coefficients applied to three-residue catalytic sites and sites having four or more residues (n_T). The distance-difference descriptors enter the estimation as the transformed variable, d′ = 1/(0.1 + d), so that smaller distance differences are ‘better’ (i.e. are expected to have a positive coefficient) while avoiding singularities.