. 2005 Nov;14(11):2849–2861. doi: 10.1110/ps.051666705

Table 1.

Structural statistics and atomic RMS differences

A. Structural statistics	<SA>	()_r
RMS deviations from experimental distance restraints (Å)
All (2750)	0.041 ± 0.005	0.040
Interresidue sequential (\|i–j\| = 1) (719)	0.038 ± 0.008	0.046
Interresidue short range (1 <\|i–j\| ≤5) (825)	0.043 ± 0.005	0.035
Interresidue long range (\|i–j\| > 5) (651)	0.045 ± 0.009	0.040
Intraresidue (483)	0.008 ± 0.004	0.004
H-bonds (72)^a	0.096 ± 0.013	0.104
RMS deviation from exptl dihedral restraints (deg) (220)^b,c	1.433 ± 0.794	0.642
RMS deviation from exptl Cα restraints (ppm) (94)	0.89 ± 0.03	0.91
RMS deviation from exptl Cβ restraints (ppm) (84)	0.91 ± 0.02	0.94
RMS deviation from ³J_NHα restraints (Hz) (53)	0.61 ± 0.02	0.54
F_NOE (kcal/mol)^c	234 ± 57	219
F_tor (kcal/mol)^c	36 ± 45	5.5
F_repel (kcal/mol)^d	108 ± 23	28.2
F_L-J (kcal/mol)^e	−374 ± 21	−362
Deviations from idealized covalent geometry
Bonds (Å) (2268)	0.005 ± 0	0.004
Angles (deg) (4109)	0.621 ± 0.030	0.608
Impropers (deg) (1163)^f	0.519 ± 0.063	0.483
PROCHECK^g
Overall G-factor	−0.11 ± 0.03	−0.16
% Residues in most favorable region of Ramachandran plot	83.5 ± 2.5	82.2
H-bond energy	1.0 ± 0.06	0.90
No. of bad contacts/100 residues	14.2 ± 2.1	9.8

B. Atomic RMS differences (Å)
	Residues 6–142		Secondary structure^h
	Backbone atoms	All atoms	Backbone atoms	All atoms
The notation of the structures is as follows: <SA> are the final 30 simulated annealing structures; is the mean structure obtained by averaging the coordinates of the individual structures best fit to each other (excluding residues 1–3, 82–89, and 112–123); and ()_r is the restrained minimized mean structure obtained by restrained minimization of the mean structure SA (Nilges et al. 1988a). The number of terms for the various restraints is given in parentheses.
^a For backbone NH-CO hydrogen bond there are two restraints: r_NH-O = 1.5–2.3 Å and r_N-O = 2.5–3.3 Å. All hydrogen bonds involve slowly exchanging NH protons.
^b The torsion angle restraints comprise 110 φ and 110 ψ.
^c The values of the square-well NOE (F_NOE) and torsion angle (F_tor) potentials (cf. Equations 2 and 3 in Clore et al. 1986) are calculated with force constants of 50 kcal mol⁻¹ Å ⁻² and 200 kcal mol⁻¹ rad⁻², respectively.
^d The value of the quartic van der Waals repulsion term (F_rep) (cf. Equation 5 in Nilges et al. 1988c) is calculated with a force constant of 4 kcal mol⁻¹ Å ⁻⁴ with the hard-sphere van der Waals radius set to 0.8 times the standard values used in the CHARMM (Brooks et al. 1983) empirical energy function (Nilges et al. 1988a,b,c).
^e E_L-J is the Lennard-Jones-van der Waals energy calculated with the CHARMM empirical energy function and is not included in the target function for simulated annealing or restrained minimization.
^f The improper torsion restraints serve to maintain planarity and chirality.
^g These were calculated by using the PROCHECK program.
^h The residues in the regular secondary structure are 17–36(α₁), 39–45(α₂), 58–72(α₃), 101–108(α₄), 4–10(β₁), 49–54(β₂), 75–78(β₃) and 92–98(β₄).
<SA>vs ()	0.41 ± 0.06	1.00 ± 0.07	0.33 ± 0.04	0.94 ± 0.08
<SA>vs ()_r	0.49 ± 0.07	1.17 ± 0.11	0.41 ± 0.05	1.09 ± 0.15
(SA)r vs	0.27	0.61	0.25	0.57