CreatePredAlphaCost pred_alpha2k alpha11 T0255.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0255.t04.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \ phobic_fit 2 \ sidechain 6 \ bystroff 5 \ soft_clashes 10 backbone_clashes 2 \ break 20 \ pred_alpha2k 3 \ pred_alpha04 6 \ 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 T0255.t04.dssp-ehl2.constraints StrandConstraint I7 W10 7.078 HelixConstraint A14 T25 7.086 StrandConstraint V31 H35 6.148 StrandConstraint V49 V56 7.614 StrandConstraint P60 L64 6.115 StrandConstraint F76 A81 7.446 HelixConstraint Q85 D97 8.002 StrandConstraint C105 R109 6.264 StrandConstraint S115 I118 8.192 HelixConstraint L123 A126 7.172 HelixConstraint R132 T144 6.281 HelixConstraint I150 F157 8.089 # file generated by validate2rr # based on 280 inputs # using the /projects/compbio/experiments/protein-predict/casp6/networks/NN280-240n300.net.28 network # limited to score of .30 or greater. # The score is an approximation of the probability Constraint W107.CB Q117.CB -10. 7.0 14.0 0.841 Constraint W10.CB Q117.CB -10. 7.0 14.0 0.724 Constraint W10.CB W107.CB -10. 7.0 14.0 0.695 Constraint Y11.CB I114.CB -10. 7.0 14.0 0.69 Constraint Y11.CB G63.CA -10. 7.0 14.0 0.682 Constraint W92.CB W107.CB -10. 7.0 14.0 0.628 Constraint W10.CB S115.CB -10. 7.0 14.0 0.622 Constraint S103.CB P120.CB -10. 7.0 14.0 0.616 Constraint W92.CB C105.CB -10. 7.0 14.0 0.616 Constraint F54.CB W107.CB -10. 7.0 14.0 0.593 bonus Constraint W10.CB F54.CB -10. 7.0 14.0 0.585 bonus Constraint C105.CB L123.CB -10. 7.0 14.0 0.576 bonus Constraint F54.CB L64.CB -10. 7.0 14.0 0.573 bonus Constraint A104.CB P120.CB -10. 7.0 14.0 0.546 bonus Constraint G63.CA I95.CB -10. 7.0 14.0 0.537 bonus Constraint F70.CB Q117.CB -10. 7.0 14.0 0.531 bonus Constraint C61.CB T88.CB -10. 7.0 14.0 0.531 bonus Constraint A19.CB V52.CB -10. 7.0 14.0 0.519 bonus Constraint W107.CB P120.CB -10. 7.0 14.0 0.517 bonus Constraint R55.CB W112.CB -10. 7.0 14.0 0.514 bonus Constraint E74.CB G100.CA -10. 7.0 14.0 0.502 bonus Constraint F54.CB Q117.CB -10. 7.0 14.0 0.498 bonus Constraint Q85.CB W107.CB -10. 7.0 14.0 0.483 bonus Constraint T51.CB L64.CB -10. 7.0 14.0 0.475 bonus Constraint E53.CB L64.CB -10. 7.0 14.0 0.469 bonus Constraint Q85.CB P120.CB -10. 7.0 14.0 0.466 bonus Constraint F54.CB C105.CB -10. 7.0 14.0 0.445 bonus Constraint S29.CB Q85.CB -10. 7.0 14.0 0.442 bonus Constraint Y11.CB W107.CB -10. 7.0 14.0 0.442 bonus Constraint T51.CB L62.CB -10. 7.0 14.0 0.439 bonus Constraint W10.CB L64.CB -10. 7.0 14.0 0.43 bonus Constraint Q85.CB A104.CB -10. 7.0 14.0 0.427 bonus Constraint W10.CB W92.CB -10. 7.0 14.0 0.427 bonus Constraint I95.CB Q117.CB -10. 7.0 14.0 0.424 bonus Constraint A75.CB Q117.CB -10. 7.0 14.0 0.424 bonus Constraint F76.CB L91.CB -10. 7.0 14.0 0.412 bonus Constraint C105.CB T119.CB -10. 7.0 14.0 0.404 bonus Constraint Q85.CB C105.CB -10. 7.0 14.0 0.401 bonus Constraint W92.CB Q117.CB -10. 7.0 14.0 0.395 bonus Constraint K111.CB P120.CB -10. 7.0 14.0 0.392 bonus Constraint G63.CA L91.CB -10. 7.0 14.0 0.392 bonus Constraint G106.CA S115.CB -10. 7.0 14.0 0.386 bonus Constraint W10.CB G67.CA -10. 7.0 14.0 0.386 bonus Constraint L64.CB C105.CB -10. 7.0 14.0 0.384 bonus Constraint D28.CB E74.CB -10. 7.0 14.0 0.384 bonus Constraint T25.CB I95.CB -10. 7.0 14.0 0.384 bonus Constraint W10.CB E53.CB -10. 7.0 14.0 0.384 bonus Constraint E102.CB R121.CB -10. 7.0 14.0 0.378 bonus Constraint N98.CB K111.CB -10. 7.0 14.0 0.378 bonus Constraint A75.CB W107.CB -10. 7.0 14.0 0.37 bonus Constraint L50.CB L62.CB -10. 7.0 14.0 0.367 bonus Constraint W10.CB G63.CA -10. 7.0 14.0 0.367 bonus Constraint E74.CB W112.CB -10. 7.0 14.0 0.358 bonus Constraint G63.CA F76.CB -10. 7.0 14.0 0.356 bonus Constraint C105.CB P120.CB -10. 7.0 14.0 0.35 bonus Constraint W10.CB S77.CB -10. 7.0 14.0 0.35 bonus Constraint G67.CA W107.CB -10. 7.0 14.0 0.347 bonus Constraint I59.CB W107.CB -10. 7.0 14.0 0.347 bonus Constraint W10.CB L91.CB -10. 7.0 14.0 0.345 bonus Constraint C105.CB Q117.CB -10. 7.0 14.0 0.342 bonus Constraint W107.CB T119.CB -10. 7.0 14.0 0.339 bonus Constraint G67.CA P120.CB -10. 7.0 14.0 0.339 bonus Constraint W10.CB N65.CB -10. 7.0 14.0 0.337 bonus Constraint W10.CB F70.CB -10. 7.0 14.0 0.334 bonus Constraint D28.CB M57.CB -10. 7.0 14.0 0.331 bonus Constraint E53.CB F70.CB -10. 7.0 14.0 0.329 bonus Constraint W10.CB A75.CB -10. 7.0 14.0 0.326 bonus Constraint R55.CB A75.CB -10. 7.0 14.0 0.323 bonus Constraint D28.CB E101.CB -10. 7.0 14.0 0.323 bonus Constraint F70.CB S115.CB -10. 7.0 14.0 0.318 bonus Constraint C105.CB I118.CB -10. 7.0 14.0 0.316 bonus Constraint Q79.CB Q117.CB -10. 7.0 14.0 0.316 bonus Constraint E74.CB P120.CB -10. 7.0 14.0 0.313 bonus Constraint I59.CB Q117.CB -10. 7.0 14.0 0.308 bonus Constraint C8.CB Q117.CB -10. 7.0 14.0 0.308 bonus Constraint C61.CB T82.CB -10. 7.0 14.0 0.305 bonus Constraint I95.CB I114.CB -10. 7.0 14.0 0.303 bonus Constraint R55.CB Q117.CB -10. 7.0 14.0 0.3 bonus Constraint P27.CB A75.CB -10. 7.0 14.0 0.3 bonus