Supplementary Table S1 Summary of structure calculation data for correct and flawed families. Backbone RMSDs values for the various structures are also shown. The “Backbone RMSD” column contains RMSD values within the bundle of conformers. The “RMSD to the reference” is the RMSD of the flawed structure with respect to the first model of the reference structure.

Structure / Total meaningful distance constraints / Average number of distance constraints violated > 0.3 Ǻ / Total meaningful angle constraints / Average number of violated  constraints / Average number of violated  constraints / Backbone RMSD (Ǻ) / RMSD to the reference (Ǻ)
PDZ (1Y7N) / - / - / - / - / - / 0.69 / -
PDZ Recalc / 1725 / 7±1 / 95 / 0 / 0 / 0.81 / 0.60
PDZ perturbed 25% / 1725 / 31±1 / 95 / 9±1 / 10±1 / 0.98 / 1.71
PDZ perturbed 50% / “ / 990±20 / “ / 24±7 / 24±7 / 0.61 / 2.39
PDZ perturbed 75% / “ / 1356±5 / “ / 31±2 / 28±2 / 0.79 / 2.59
Calb D9k (1KQV) / - / - / - / - / 0.66 / -
Calb D9k minimized / 1675 / 2±1 / 37 / 0 / - / 0.71 / 0.67
Calb D9k perturbed 25% / 1675 / 29±9 / 37 / 16±1 / - / 0.67 / 2.56
Calb D9k perturbed 50% / “ / 423±9 / “ / 22±2 / - / 0.84 / 2.81
Calb D9k perturbed 75% / “ / 1287±3 / “ / 21±2 / - / 1.5 / 3.09
Calb D9k Error A / “ / 0 / “ / 1±1 / - / 0.74 / 2.65
Calb D9k Error B / “ / 0.1±0.4 / “ / 1±1 / - / 0.64 / 2.67
Calb D9k Error C / “ / 12±4 / “ / 3±1 / - / 2.00 / 2.94
Menkes 6 (1YJR) / - / - / - / - / - / 1.07 / -
Menkes 6 Error / 1956 / 4±1 / 82 / 15±2 / 4±1 / 1.32 / 3.48

Supplementary table S2: Output of FRST. For each family of structures the minimum and the maximum values of composite, RAPDF, salvation, H bond and Torsion energies are shown together with average values on the families ± standard deviation

System / Composite / Rapdf / Solvation / H Bond / Torsion
1Y7N / -13710÷ -10158 / 11586± 952 / -2671÷-2504 / -2585±45 / -4.1÷-2.8 / -3.4±0.4 / -66.0÷-60.0 / -62.3±-1.7 / -23.4÷-14.5 / -18.6±2.5
PDZ pert 25% / -11399÷ -6384 / -8763± 1004 / -2202÷-2018 / -2103±39 / -5.2÷-3.7 / -4.5±0.3 / -64.0÷-59.0 / -61.6±1.1 / -19.1÷-5.70 / -12.4±2.8
PDZ pert 50% / -4600÷ -880 / -2815± 979 / -1786÷-1582 / -1678±50 / -6.3÷-4.7 / -5.3±0.4 / -61.0÷-58.0 / -59.8±0.7 / -2.31÷8.00 / 3.1±3.0
PDZ pert 75% / 1068÷ 3277 / 1129± 995 / -1106÷-917 / -1031±46 / -6.2÷-4.6 / -5.3±0.4 / -66.0÷-58.0 / -60.5±1.7 / 2.38÷14.51 / 9.5±2.7
Calb D9k(1KQV) / -9927÷ -5947 / -7488± 853 / -3127÷-2843 / -2987±72 / -8.2÷-6.5 / -7.5±0.4 / -59.0÷-54.0 / -56.0±1.0 / -3.09÷7.22 / 2.7±2.4
Calb pert 25% / -11701÷-5782 / -8915± 1053 / -3135÷-2838 / -3006±70 / -7.9÷-5.8 / -7.1±0.5 / -55.0÷-49.0 / -52.5±1.5 / -7.87÷7.34 / -1.3±2.7
Calb pert 50% / -9550÷-6559 / -8265± 690 / -2764÷-2582 / -2689±38 / -6.9÷-5.4 / -6.3±0.3 / -60.0÷56.0 / -58.5±0.8 / -6.93÷1.92 / -3.8±2.0
Calb pert 75% / -2850÷ -183 / -1154± 598 / -2012÷-1859 / -1945±34 / -4.7÷-3.0 / 4.2±0.3 / -60.0÷-55 / -58.2±1.6 / 3.37÷11.51 / 8.4±1.7
Calb Err A / -10306÷ -5907 / -8677± 1170 / -3036 ÷-2323 / -2627±142 / -8.2÷-5.2 / -6.6±0.71 / -62.0÷-52.0 / -59.0±2.5 / -9.12÷0.87 / -5.00±2.71
Calb Err B / -10621÷ -5338 / -8063÷ 1334 / -2901÷-2667 / -2626±147 / -7.8÷-5.4 / -6.3±0.6 / -63.0÷-55.0 / -58.6±2.0 / -10.18÷3.24 / -3.59±3.29
Calb Err C / -8848÷ +602 / -3650÷ 2662 / -2309÷-1127 / -1817±327 / -8.4÷-1.6 / -5.4±1.9 / -57.0÷-51.0 / -55.0±1.7 / -6.25÷11.50 / 2.43±4.80
Menkes 6 (1YJR) / -9325÷ -1429 / -5597± 1646 / -2784÷-2335 / -2581±99 / -3.2÷-0.6 / -1.9±0.6 / -62.0÷-52.0 / -56.4±2.6 / -11.25÷6.09 / -2.85±4.12
Menkes 6 Err / -7564 +15÷ / -4788± 1777 / -2827÷-2185 / -2460±160 / -5.5÷-2.8 / -4.2±0.7 / -63.0÷-52.0 / -56.7±3.1 / -7.15÷15.5 / 1.80±5.20