CreatePredAlphaCost pred_alpha2k alpha11 T0270.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0270.t04.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 5 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 1 \ bystroff 5 \ soft_clashes 10 backbone_clashes 2 \ break 20 \ pred_alpha2k 5 \ pred_alpha04 1 \ constraints 10 \ hbond_geom 1 \ hbond_geom_backbone 1 \ hbond_geom_beta 5 \ hbond_geom_beta_pair 10 // Add the following for extra-cellular proteins: # known_ssbond 0.5 # and put ssbond command in constraints file # maybe_ssbond 0.5 // For comparative modeling, increase weight of break and hbond_geom... // put any constraints here, such as helix constraints, strand constraints, // sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms. # from T0270.t2k.dssp-ehl2.constraints HelixConstraint F26 W29 7.284 HelixConstraint L34 E53 6.876 HelixConstraint L83 S96 6.156 HelixConstraint F98 R100 6.345 HelixConstraint V128 R131 6.109 HelixConstraint A162 K178 6.048 HelixConstraint P207 G227 6.605 HelixConstraint E240 F246 7.519 StrandConstraint Y62 V67 6.315 StrandConstraint L74 N78 6.37 StrandConstraint Y106 E113 6.398 StrandConstraint Y141 Y145 6.55 StrandConstraint M184 Q191 6.011 StrandConstraint E197 F203 6.93 StrandConstraint F232 V234 6.351 # Sheet Constraints from try12 SheetConstraint D73 F76 F108 V111 hbond L75 10 SheetConstraint S116 E118 G176 K178 hbond Q117 10 SheetConstraint G140 C143 Q154 R151 hbond Y141 10 # Constraints used in try12.costfcn that are close in try12-opt2 and # predicted to be strands (str2) SheetConstraint (T0270)G14 (T0270)D20 (T0270)S204 (T0270)W198 hbond (T0270)H16 10 SheetConstraint (T0270)W15 (T0270)D20 (T0270)Y237 (T0270)F232 hbond (T0270)V17 10 SheetConstraint (T0270)Y62 (T0270)I64 (T0270)D201 (T0270)G199 hbond (T0270)Y62 4 SheetConstraint (T0270)E113 (T0270)L114 (T0270)G199 (T0270)W198 hbond (T0270)E113 4 # file generated by validate2rr # based on 280 inputs # using the NN280-240n300.net.28 network # limited to score of .30 or greater. # The score is an approximation of the probability Constraint I187.CB D201.CB -10. 7.0 14.0 0.647 Constraint L18.CB F144.CB -10. 7.0 14.0 0.647 Constraint L202.CB I213.CB -10. 7.0 14.0 0.611 Constraint C143.CB Y226.CB -10. 7.0 14.0 0.611 Constraint L79.CB Y226.CB -10. 7.0 14.0 0.599 bonus Constraint V67.CB F108.CB -10. 7.0 14.0 0.576 bonus Constraint F144.CB I187.CB -10. 7.0 14.0 0.549 bonus Constraint R22.CB Y179.CB -10. 7.0 14.0 0.546 bonus Constraint F144.CB G176.CA -10. 7.0 14.0 0.543 bonus Constraint D201.CB Y226.CB -10. 7.0 14.0 0.478 bonus Constraint Q66.CB D122.CB -10. 7.0 14.0 0.478 bonus Constraint L75.CB V186.CB -10. 7.0 14.0 0.472 bonus Constraint L202.CB Y226.CB -10. 7.0 14.0 0.46 bonus Constraint L18.CB V186.CB -10. 7.0 14.0 0.442 bonus Constraint L74.CB V186.CB -10. 7.0 14.0 0.439 bonus Constraint R28.CB F108.CB -10. 7.0 14.0 0.43 bonus Constraint F108.CB D201.CB -10. 7.0 14.0 0.427 bonus Constraint Q185.CB Y215.CB -10. 7.0 14.0 0.424 bonus Constraint L74.CB F144.CB -10. 7.0 14.0 0.424 bonus Constraint G199.CA V214.CB -10. 7.0 14.0 0.421 bonus Constraint Q66.CB F108.CB -10. 7.0 14.0 0.421 bonus Constraint I187.CB Y226.CB -10. 7.0 14.0 0.418 bonus Constraint Y145.CB E197.CB -10. 7.0 14.0 0.418 bonus Constraint E90.CB F108.CB -10. 7.0 14.0 0.415 bonus Constraint L18.CB L202.CB -10. 7.0 14.0 0.415 bonus Constraint F144.CB L202.CB -10. 7.0 14.0 0.404 bonus Constraint F144.CB G230.CA -10. 7.0 14.0 0.401 bonus Constraint Y215.CB A224.CB -10. 7.0 14.0 0.395 bonus Constraint F144.CB Y226.CB -10. 7.0 14.0 0.395 bonus Constraint D220.CB F229.CB -10. 7.0 14.0 0.389 bonus Constraint W198.CB F232.CB -10. 7.0 14.0 0.389 bonus Constraint A27.CB F108.CB -10. 7.0 14.0 0.389 bonus Constraint F219.CB G230.CA -10. 7.0 14.0 0.386 bonus Constraint M147.CB V200.CB -10. 7.0 14.0 0.386 bonus Constraint Y127.CB K211.CB -10. 7.0 14.0 0.37 bonus Constraint V186.CB L202.CB -10. 7.0 14.0 0.364 bonus Constraint Q185.CB S223.CB -10. 7.0 14.0 0.358 bonus Constraint I187.CB V222.CB -10. 7.0 14.0 0.353 bonus Constraint Q185.CB A224.CB -10. 7.0 14.0 0.353 bonus Constraint K71.CB R225.CB -10. 7.0 14.0 0.35 bonus Constraint M147.CB V234.CB -10. 7.0 14.0 0.347 bonus Constraint L44.CB L79.CB -10. 7.0 14.0 0.339 bonus Constraint R28.CB L121.CB -10. 7.0 14.0 0.337 bonus Constraint D220.CB G230.CA -10. 7.0 14.0 0.334 bonus Constraint Y215.CB F229.CB -10. 7.0 14.0 0.331 bonus Constraint L18.CB L168.CB -10. 7.0 14.0 0.331 bonus Constraint Y215.CB R225.CB -10. 7.0 14.0 0.329 bonus Constraint Q185.CB F229.CB -10. 7.0 14.0 0.329 bonus Constraint F144.CB I213.CB -10. 7.0 14.0 0.329 bonus Constraint E90.CB L121.CB -10. 7.0 14.0 0.329 bonus Constraint V186.CB Y226.CB -10. 7.0 14.0 0.326 bonus Constraint H19.CB G189.CA -10. 7.0 14.0 0.323 bonus Constraint L18.CB Y226.CB -10. 7.0 14.0 0.323 bonus Constraint K211.CB F229.CB -10. 7.0 14.0 0.318 bonus Constraint S188.CB Y215.CB -10. 7.0 14.0 0.318 bonus Constraint D25.CB L83.CB -10. 7.0 14.0 0.318 bonus Constraint L18.CB L75.CB -10. 7.0 14.0 0.318 bonus Constraint D201.CB F210.CB -10. 7.0 14.0 0.313 bonus Constraint L18.CB L74.CB -10. 7.0 14.0 0.31 bonus Constraint K211.CB D220.CB -10. 7.0 14.0 0.308 bonus Constraint Q185.CB R225.CB -10. 7.0 14.0 0.308 bonus Constraint M159.CB Q185.CB -10. 7.0 14.0 0.308 bonus Constraint F144.CB V186.CB -10. 7.0 14.0 0.308 bonus Constraint F21.CB L83.CB -10. 7.0 14.0 0.308 bonus Constraint F144.CB V200.CB -10. 7.0 14.0 0.303 bonus Constraint K71.CB F229.CB -10. 7.0 14.0 0.303 bonus Constraint K71.CB Q185.CB -10. 7.0 14.0 0.303 bonus Constraint H19.CB D201.CB -10. 7.0 14.0 0.303 bonus Constraint L202.CB R225.CB -10. 7.0 14.0 0.3 bonus Constraint V186.CB R225.CB -10. 7.0 14.0 0.3 bonus Constraint H70.CB Q209.CB -10. 7.0 14.0 0.3 bonus