CreatePredAlphaCost pred_alpha2k alpha11 T0219.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0219.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 2 \ pred_alpha04 4 \ constraints 25 \ hbond_geom 1.0 \ hbond_geom_backbone 1.0 \ hbond_geom_beta 5.0 \ hbond_geom_beta_pair 15.0 // 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. include T0219.t2k.dssp-ehl2.constraints include T0219.t2k.dssp-ebghstl.constraints include T0219.t2k.stride-ebghtl.constraints include T0219.t2k.str2.constraints include T0219.t2k.alpha.constraints include T0219.t2k.bys.constraints include T0219.t04.dssp-ehl2.constraints include T0219.t04.dssp-ebghstl.constraints include T0219.t04.stride-ebghtl.constraints include T0219.t04.str2.constraints include T0219.t04.alpha.constraints include T0219.t04.bys.constraints # for the metal binding site, constrain the strongly conserved residues # with desired measurements from the 1mzeA template Constraint D147.OD1 H145.NE2 0 3.824 6.8 1 Constraint D147.OD2 H224.NE2 0 2.943 5.9 1 Constraint H224.NE2 H145.NE2 0 3.233 6.2 1 # Define all the strands, but only emphasize the ones that are having # trouble forming, since the sheet constraints should get the rest. StrandConstraint T5 S7 1 StrandConstraint E10 S11 1 StrandConstraint L31 R34 1 StrandConstraint Y59 V66 1 StrandConstraint F81 A88 1 StrandConstraint G95 T103 4 # s6 did not appear spontaneously StrandConstraint K130 K137 1 StrandConstraint G140 F142 1 StrandConstraint A144 F146 1 StrandConstraint Y149 Q157 1 StrandConstraint E159 K166 1 StrandConstraint A205 T211 1 StrandConstraint T214 P219 1 StrandConstraint W223 S228 1 StrandConstraint T232 G240 1 # Sheet constraints, mostly from 1mzeA alignment, as improved by tries # from alignment to 1mzeA SheetConstraint T5 V8 A205 V208 hbond E6 5 # s1 || s11 SheetConstraint E10 S11 V32 A33 hbond S11 10 # s2 || s3 SheetConstraint L31 R34 Y217 T214 hbond A33 10 # s3 ^v s12 # from try1-opt2 SheetConstraint Y59 V66 A88 F81 hbond V63 10 # s4 ^v s5 # add two constraints to insert one strand (S6) antiparallel between two others (S4,S7) SheetConstraint Y59 V66 F102 G95 hbond M64 10 # s4 ^v s6 SheetConstraint A96 T103 K137 K130 hbond L98 5 # s6 ^v s7 # from try1-opt2 SheetConstraint K130 K137 T238 A231 hbond Y134 5 # s7 ^v s14 # from alignment to 1mzeA # kink not needed in strand without Pro at 143, so combine constraints? SheetConstraint G140 F142 S228 T226 hbond F142 5 # s8a ^v s13 SheetConstraint A144 F146 S225 W223 hbond H145 5 # s8b ^b s13 # from alignment to 1mzeA SheetConstraint Y149 Q157 G240 T232 hbond T150 5 # s9 ^v s14 SheetConstraint T150 Q155 P219 T214 hbond N151 5 # s9 ^v s12 SheetConstraint E159 A165 T211 A205 hbond K160 5 # s10 ^v s11 SheetConstraint E159 K166 D229 L222 hbond T161 5 # s10 ^v s13 # file generated by validate2rr # based on 280 inputs # using the NN280-240n300.net.28 network # limited to score of .35 or greater or # the best 10 scores # The score is an approximation of the probability Constraint V133.CB S225.CB -10. 7.0 12.0 0.932 Constraint P219.CB L245.CB -10. 7.0 12.0 0.908 Constraint F154.CB Y217.CB -10. 7.0 12.0 0.895 Constraint L218.CB L235.CB -10. 7.0 12.0 0.883 Constraint F146.CB Q155.CB -10. 7.0 12.0 0.86 Constraint I156.CB L222.CB -10. 7.0 12.0 0.855 Constraint T161.CB D229.CB -10. 7.0 12.0 0.853 Constraint I156.CB A234.CB -10. 7.0 12.0 0.853 Constraint A148.CB W244.CB -10. 7.0 12.0 0.853 Constraint F154.CB I237.CB -10. 7.0 12.0 0.85 Constraint F154.CB T238.CB -10. 7.0 12.0 0.848 Constraint I156.CB P219.CB -10. 7.0 12.0 0.847 Constraint D147.CB P219.CB -10. 7.0 12.0 0.845 Constraint Q155.CB L216.CB -10. 7.0 12.0 0.842 Constraint D147.CB I156.CB -10. 7.0 12.0 0.842 Constraint A148.CB I237.CB -10. 7.0 12.0 0.841 Constraint A136.CB I153.CB -10. 7.0 12.0 0.837 Constraint D147.CB N236.CB -10. 7.0 12.0 0.832 Constraint Y217.CB I237.CB -10. 7.0 12.0 0.831 Constraint G141.CA S225.CB -10. 7.0 12.0 0.829 Constraint I156.CB N236.CB -10. 7.0 12.0 0.826 Constraint A148.CB K160.CB -10. 7.0 12.0 0.824 Constraint G141.CA K227.CB -10. 7.0 12.0 0.82 Constraint R220.CB L245.CB -10. 7.0 12.0 0.819 Constraint A148.CB K163.CB -10. 7.0 12.0 0.815 Constraint Y217.CB N236.CB -10. 7.0 12.0 0.813 Constraint Y134.CB L210.CB -10. 7.0 12.0 0.813 Constraint K160.CB V208.CB -10. 7.0 12.0 0.811 Constraint Q155.CB W223.CB -10. 7.0 12.0 0.809 Constraint A136.CB K160.CB -10. 7.0 12.0 0.808 Constraint A136.CB Q155.CB -10. 7.0 12.0 0.806 Constraint P219.CB N236.CB -10. 7.0 12.0 0.804 Constraint G140.CA T238.CB -10. 7.0 12.0 0.802 Constraint I156.CB S228.CB -10. 7.0 12.0 0.8