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 8 near_backbone 8 way_back 8 dry5 15 dry6.5 20 dry8 15 dry12 6 \ phobic_fit 2 \ sidechain 6 \ bystroff 5 \ soft_clashes 20 backbone_clashes 2 \ break 40 \ pred_alpha2k 2 \ pred_alpha04 4 \ constraints 10 \ 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. #from T0219.t04.dssp-ehl2.constraints HelixConstraint M18 Y25 0.6409 HelixConstraint V49 L56 0.7359 HelixConstraint E87 W91 0.628 HelixConstraint I107 E120 0.6923 HelixConstraint L189 Q190 0.622 HelixConstraint P242 K255 0.689 HelixConstraint F262 L265 0.6154 HelixConstraint K277 E293 0.7039 HelixConstraint A295 E296 0.6554 HelixConstraint P300 Q305 0.6197 HelixConstraint Q318 L325 0.6376 # 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 .30 or greater. # The score is an approximation of the probability Constraint V133.CB S225.CB -10. 7.0 14.0 0.932 Constraint P219.CB L245.CB -10. 7.0 14.0 0.908 Constraint F154.CB Y217.CB -10. 7.0 14.0 0.895 Constraint L218.CB L235.CB -10. 7.0 14.0 0.883 Constraint F146.CB Q155.CB -10. 7.0 14.0 0.86 Constraint I156.CB L222.CB -10. 7.0 14.0 0.855 Constraint T161.CB D229.CB -10. 7.0 14.0 0.853 Constraint I156.CB A234.CB -10. 7.0 14.0 0.853 Constraint A148.CB W244.CB -10. 7.0 14.0 0.853 Constraint F154.CB I237.CB -10. 7.0 14.0 0.85 Constraint F154.CB T238.CB -10. 7.0 14.0 0.848 Constraint I156.CB P219.CB -10. 7.0 14.0 0.847 Constraint D147.CB P219.CB -10. 7.0 14.0 0.845 Constraint Q155.CB L216.CB -10. 7.0 14.0 0.842 Constraint D147.CB I156.CB -10. 7.0 14.0 0.842 Constraint A148.CB I237.CB -10. 7.0 14.0 0.841 Constraint A136.CB I153.CB -10. 7.0 14.0 0.837 Constraint D147.CB N236.CB -10. 7.0 14.0 0.832 Constraint Y217.CB I237.CB -10. 7.0 14.0 0.831 Constraint G141.CA S225.CB -10. 7.0 14.0 0.829 Constraint I156.CB N236.CB -10. 7.0 14.0 0.826 Constraint A148.CB K160.CB -10. 7.0 14.0 0.824 Constraint G141.CA K227.CB -10. 7.0 14.0 0.82 Constraint R220.CB L245.CB -10. 7.0 14.0 0.819 Constraint A148.CB K163.CB -10. 7.0 14.0 0.815 Constraint Y217.CB N236.CB -10. 7.0 14.0 0.813 Constraint Y134.CB L210.CB -10. 7.0 14.0 0.813 Constraint K160.CB V208.CB -10. 7.0 14.0 0.811 Constraint Q155.CB W223.CB -10. 7.0 14.0 0.809 Constraint A136.CB K160.CB -10. 7.0 14.0 0.808 Constraint A136.CB Q155.CB -10. 7.0 14.0 0.806 Constraint P219.CB N236.CB -10. 7.0 14.0 0.804 Constraint G140.CA T238.CB -10. 7.0 14.0 0.802 Constraint I156.CB S228.CB -10. 7.0 14.0 0.8 Constraint Q155.CB L210.CB -10. 7.0 14.0 0.798 Constraint I156.CB L233.CB -10. 7.0 14.0 0.796 Constraint Q155.CB S225.CB -10. 7.0 14.0 0.794 Constraint A148.CB T226.CB -10. 7.0 14.0 0.79 Constraint A136.CB S228.CB -10. 7.0 14.0 0.79 Constraint F154.CB L210.CB -10. 7.0 14.0 0.788 Constraint F142.CB Q155.CB -10. 7.0 14.0 0.786 Constraint K160.CB S228.CB -10. 7.0 14.0 0.78 Constraint A148.CB W162.CB -10. 7.0 14.0 0.78 Constraint S225.CB L235.CB -10. 7.0 14.0 0.778 Constraint A135.CB L233.CB -10. 7.0 14.0 0.778 Constraint F142.CB T226.CB -10. 7.0 14.0 0.774 Constraint I156.CB L235.CB -10. 7.0 14.0 0.772 Constraint A148.CB N236.CB -10. 7.0 14.0 0.77 Constraint D147.CB T161.CB -10. 7.0 14.0 0.77 Constraint F142.CB I156.CB -10. 7.0 14.0 0.77 Constraint N151.CB I237.CB -10. 7.0 14.0 0.765 Constraint K143.CB S225.CB -10. 7.0 14.0 0.763 Constraint S225.CB M248.CB -10. 7.0 14.0 0.761 Constraint L152.CB L245.CB -10. 7.0 14.0 0.761 Constraint T226.CB N236.CB -10. 7.0 14.0 0.759 Constraint Q155.CB S228.CB -10. 7.0 14.0 0.759 Constraint K137.CB V170.CB -10. 7.0 14.0 0.759 Constraint T226.CB L235.CB -10. 7.0 14.0 0.757 Constraint G140.CA I153.CB -10. 7.0 14.0 0.757 Constraint T161.CB I207.CB -10. 7.0 14.0 0.752 Constraint D147.CB K160.CB -10. 7.0 14.0 0.752 Constraint Y134.CB W244.CB -10. 7.0 14.0 0.752 Constraint L152.CB I237.CB -10. 7.0 14.0 0.75 Constraint K137.CB Q155.CB -10. 7.0 14.0 0.75 Constraint I237.CB M248.CB -10. 7.0 14.0 0.745 Constraint T150.CB N236.CB -10. 7.0 14.0 0.745 Constraint A148.CB K227.CB -10. 7.0 14.0 0.745 Constraint F142.CB F154.CB -10. 7.0 14.0 0.745 Constraint I156.CB T226.CB -10. 7.0 14.0 0.743 Constraint A136.CB F154.CB -10. 7.0 14.0 0.743 Constraint S225.CB I237.CB -10. 7.0 14.0 0.741 Constraint N151.CB N236.CB -10. 7.0 14.0 0.741 Constraint A136.CB P219.CB -10. 7.0 14.0 0.741 Constraint S129.CB L247.CB -10. 7.0 14.0 0.741 Constraint F154.CB A234.CB -10. 7.0 14.0 0.739 Constraint F154.CB L164.CB -10. 7.0 14.0 0.739 Constraint T226.CB T238.CB -10. 7.0 14.0 0.736 Constraint I153.CB L210.CB -10. 7.0 14.0 0.734 Constraint I156.CB M215.CB -10. 7.0 14.0 0.729 Constraint D147.CB I237.CB -10. 7.0 14.0 0.729 Constraint F142.CB T238.CB -10. 7.0 14.0 0.729 Constraint A136.CB K227.CB -10. 7.0 14.0 0.729 Constraint I153.CB L216.CB -10. 7.0 14.0 0.727 Constraint N151.CB L210.CB -10. 7.0 14.0 0.727 Constraint Q155.CB T238.CB -10. 7.0 14.0 0.724 Constraint F146.CB N236.CB -10. 7.0 14.0 0.724 Constraint A136.CB L210.CB -10. 7.0 14.0 0.724 Constraint A135.CB N236.CB -10. 7.0 14.0 0.724 Constraint V133.CB Q155.CB -10. 7.0 14.0 0.722 Constraint V133.CB I153.CB -10. 7.0 14.0 0.722 Constraint F142.CB K160.CB -10. 7.0 14.0 0.72 Constraint W162.CB I237.CB -10. 7.0 14.0 0.717 Constraint A135.CB L164.CB -10. 7.0 14.0 0.715 Constraint L210.CB S225.CB -10. 7.0 14.0 0.712 Constraint N151.CB Y217.CB -10. 7.0 14.0 0.71 Constraint A148.CB S228.CB -10. 7.0 14.0 0.71 Constraint I156.CB T238.CB -10. 7.0 14.0 0.707 Constraint F142.CB L235.CB -10. 7.0 14.0 0.707 Constraint K137.CB K227.CB -10. 7.0 14.0 0.707 Constraint T226.CB I237.CB -10. 7.0 14.0 0.705 Constraint F142.CB I153.CB -10. 7.0 14.0 0.705 Constraint M215.CB N236.CB -10. 7.0 14.0 0.702 Constraint K160.CB L245.CB -10. 7.0 14.0 0.702 Constraint F154.CB T226.CB -10. 7.0 14.0 0.702 Constraint N151.CB A234.CB -10. 7.0 14.0 0.702 Constraint T150.CB I237.CB -10. 7.0 14.0 0.702 Constraint W162.CB L218.CB -10. 7.0 14.0 0.7 Constraint L152.CB L164.CB -10. 7.0 14.0 0.7 Constraint K160.CB P219.CB -10. 7.0 14.0 0.697 bonus Constraint L152.CB T238.CB -10. 7.0 14.0 0.697 bonus Constraint T226.CB Q241.CB -10. 7.0 14.0 0.695 bonus Constraint S225.CB W244.CB -10. 7.0 14.0 0.695 bonus Constraint A144.CB L235.CB -10. 7.0 14.0 0.695 bonus Constraint A144.CB S225.CB -10. 7.0 14.0 0.695 bonus Constraint A148.CB L164.CB -10. 7.0 14.0 0.692 bonus Constraint L31.CB A136.CB -10. 7.0 14.0 0.692 bonus Constraint I153.CB I237.CB -10. 7.0 14.0 0.69 bonus Constraint A148.CB Q241.CB -10. 7.0 14.0 0.69 bonus Constraint A148.CB L218.CB -10. 7.0 14.0 0.69 bonus Constraint A131.CB N236.CB -10. 7.0 14.0 0.687 bonus Constraint A131.CB A148.CB -10. 7.0 14.0 0.687 bonus Constraint I132.CB Q155.CB -10. 7.0 14.0 0.684 bonus Constraint A136.CB L235.CB -10. 7.0 14.0 0.682 bonus Constraint A136.CB A234.CB -10. 7.0 14.0 0.682 bonus Constraint A131.CB D147.CB -10. 7.0 14.0 0.682 bonus Constraint Y149.CB I237.CB -10. 7.0 14.0 0.679 bonus Constraint A148.CB L222.CB -10. 7.0 14.0 0.679 bonus Constraint K137.CB I156.CB -10. 7.0 14.0 0.679 bonus Constraint Q157.CB R220.CB -10. 7.0 14.0 0.677 bonus Constraint I156.CB K227.CB -10. 7.0 14.0 0.674 bonus Constraint F154.CB K227.CB -10. 7.0 14.0 0.674 bonus Constraint A148.CB R220.CB -10. 7.0 14.0 0.674 bonus Constraint G141.CA I153.CB -10. 7.0 14.0 0.671 bonus Constraint A135.CB F154.CB -10. 7.0 14.0 0.671 bonus Constraint A131.CB I237.CB -10. 7.0 14.0 0.671 bonus Constraint L218.CB I237.CB -10. 7.0 14.0 0.669 bonus Constraint F154.CB S228.CB -10. 7.0 14.0 0.669 bonus Constraint T150.CB L235.CB -10. 7.0 14.0 0.669 bonus Constraint A144.CB T226.CB -10. 7.0 14.0 0.669 bonus Constraint G141.CA I237.CB -10. 7.0 14.0 0.669 bonus Constraint V133.CB W244.CB -10. 7.0 14.0 0.669 bonus Constraint I132.CB A165.CB -10. 7.0 14.0 0.669 bonus Constraint S225.CB N236.CB -10. 7.0 14.0 0.666 bonus Constraint L164.CB I237.CB -10. 7.0 14.0 0.666 bonus Constraint K160.CB D229.CB -10. 7.0 14.0 0.666 bonus Constraint Q155.CB A234.CB -10. 7.0 14.0 0.666 bonus Constraint A144.CB M248.CB -10. 7.0 14.0 0.666 bonus Constraint G141.CA T226.CB -10. 7.0 14.0 0.666 bonus Constraint G141.CA M215.CB -10. 7.0 14.0 0.666 bonus Constraint I153.CB W162.CB -10. 7.0 14.0 0.663 bonus Constraint D147.CB Q157.CB -10. 7.0 14.0 0.661 bonus Constraint G141.CA F154.CB -10. 7.0 14.0 0.661 bonus Constraint A131.CB Q155.CB -10. 7.0 14.0 0.661 bonus Constraint S228.CB I237.CB -10. 7.0 14.0 0.658 bonus Constraint L152.CB L210.CB -10. 7.0 14.0 0.658 bonus Constraint F142.CB N236.CB -10. 7.0 14.0 0.658 bonus Constraint A136.CB S225.CB -10. 7.0 14.0 0.658 bonus Constraint I132.CB I156.CB -10. 7.0 14.0 0.658 bonus Constraint L235.CB W244.CB -10. 7.0 14.0 0.655 bonus Constraint F154.CB M215.CB -10. 7.0 14.0 0.655 bonus Constraint D147.CB L216.CB -10. 7.0 14.0 0.655 bonus Constraint K137.CB T161.CB -10. 7.0 14.0 0.655 bonus Constraint S225.CB A234.CB -10. 7.0 14.0 0.653 bonus Constraint L152.CB P219.CB -10. 7.0 14.0 0.653 bonus Constraint N151.CB L218.CB -10. 7.0 14.0 0.653 bonus Constraint F142.CB W244.CB -10. 7.0 14.0 0.653 bonus Constraint F142.CB S225.CB -10. 7.0 14.0 0.653 bonus Constraint S225.CB F239.CB -10. 7.0 14.0 0.65 bonus Constraint Q157.CB N236.CB -10. 7.0 14.0 0.65 bonus Constraint L152.CB N236.CB -10. 7.0 14.0 0.65 bonus Constraint D147.CB T238.CB -10. 7.0 14.0 0.65 bonus Constraint L222.CB L235.CB -10. 7.0 14.0 0.647 bonus Constraint F154.CB N236.CB -10. 7.0 14.0 0.647 bonus Constraint V133.CB Q241.CB -10. 7.0 14.0 0.647 bonus Constraint V133.CB W223.CB -10. 7.0 14.0 0.647 bonus Constraint M215.CB T226.CB -10. 7.0 14.0 0.644 bonus Constraint A148.CB S225.CB -10. 7.0 14.0 0.644 bonus Constraint T214.CB I237.CB -10. 7.0 14.0 0.642 bonus Constraint N167.CB W223.CB -10. 7.0 14.0 0.642 bonus Constraint K160.CB W244.CB -10. 7.0 14.0 0.642 bonus Constraint Q157.CB T238.CB -10. 7.0 14.0 0.642 bonus Constraint Y149.CB N236.CB -10. 7.0 14.0 0.642 bonus Constraint A136.CB L245.CB -10. 7.0 14.0 0.642 bonus Constraint A136.CB L222.CB -10. 7.0 14.0 0.642 bonus Constraint L216.CB N236.CB -10. 7.0 14.0 0.639 bonus Constraint I156.CB L245.CB -10. 7.0 14.0 0.639 bonus Constraint I153.CB L218.CB -10. 7.0 14.0 0.639 bonus Constraint L152.CB F239.CB -10. 7.0 14.0 0.639 bonus Constraint N151.CB L216.CB -10. 7.0 14.0 0.639 bonus Constraint D147.CB Y217.CB -10. 7.0 14.0 0.639 bonus Constraint F142.CB K227.CB -10. 7.0 14.0 0.636 bonus Constraint V133.CB T238.CB -10. 7.0 14.0 0.636 bonus Constraint I132.CB N236.CB -10. 7.0 14.0 0.636 bonus Constraint Q155.CB Y217.CB -10. 7.0 14.0 0.633 bonus Constraint I153.CB N236.CB -10. 7.0 14.0 0.633 bonus Constraint F142.CB A234.CB -10. 7.0 14.0 0.633 bonus Constraint G141.CA T238.CB -10. 7.0 14.0 0.633 bonus Constraint L218.CB M248.CB -10. 7.0 14.0 0.63 bonus Constraint Y217.CB T226.CB -10. 7.0 14.0 0.63 bonus Constraint M215.CB I237.CB -10. 7.0 14.0 0.63 bonus Constraint L164.CB A234.CB -10. 7.0 14.0 0.63 bonus Constraint Q155.CB N236.CB -10. 7.0 14.0 0.63 bonus Constraint I153.CB W223.CB -10. 7.0 14.0 0.63 bonus Constraint G141.CA I156.CB -10. 7.0 14.0 0.63 bonus Constraint G141.CA Q155.CB -10. 7.0 14.0 0.63 bonus Constraint S225.CB T238.CB -10. 7.0 14.0 0.628 bonus Constraint Y217.CB A234.CB -10. 7.0 14.0 0.628 bonus Constraint D147.CB L164.CB -10. 7.0 14.0 0.628 bonus Constraint F142.CB M215.CB -10. 7.0 14.0 0.628 bonus Constraint A136.CB T226.CB -10. 7.0 14.0 0.628 bonus Constraint A136.CB I156.CB -10. 7.0 14.0 0.628 bonus Constraint V133.CB I237.CB -10. 7.0 14.0 0.628 bonus Constraint I132.CB I237.CB -10. 7.0 14.0 0.628 bonus Constraint I156.CB V208.CB -10. 7.0 14.0 0.625 bonus Constraint F142.CB I237.CB -10. 7.0 14.0 0.625 bonus Constraint A148.CB Q157.CB -10. 7.0 14.0 0.622 bonus Constraint Y134.CB T238.CB -10. 7.0 14.0 0.622 bonus Constraint L164.CB L235.CB -10. 7.0 14.0 0.619 bonus Constraint L152.CB A234.CB -10. 7.0 14.0 0.619 bonus Constraint L152.CB W162.CB -10. 7.0 14.0 0.619 bonus Constraint Y149.CB L245.CB -10. 7.0 14.0 0.619 bonus Constraint Y149.CB T238.CB -10. 7.0 14.0 0.619 bonus Constraint A131.CB S225.CB -10. 7.0 14.0 0.619 bonus Constraint W162.CB T226.CB -10. 7.0 14.0 0.616 bonus Constraint N151.CB T238.CB -10. 7.0 14.0 0.616 bonus Constraint N151.CB P219.CB -10. 7.0 14.0 0.616 bonus Constraint A148.CB Y217.CB -10. 7.0 14.0 0.616 bonus Constraint G141.CA F239.CB -10. 7.0 14.0 0.616 bonus Constraint L216.CB A234.CB -10. 7.0 14.0 0.614 bonus Constraint W162.CB S225.CB -10. 7.0 14.0 0.614 bonus Constraint A135.CB L222.CB -10. 7.0 14.0 0.614 bonus Constraint P85.CB I153.CB -10. 7.0 14.0 0.614 bonus Constraint Q155.CB I237.CB -10. 7.0 14.0 0.611 bonus Constraint V133.CB A144.CB -10. 7.0 14.0 0.611 bonus Constraint M215.CB M248.CB -10. 7.0 14.0 0.608 bonus Constraint W162.CB M248.CB -10. 7.0 14.0 0.608 bonus Constraint I153.CB A234.CB -10. 7.0 14.0 0.608 bonus Constraint L152.CB L216.CB -10. 7.0 14.0 0.608 bonus Constraint A148.CB G240.CA -10. 7.0 14.0 0.608 bonus Constraint F146.CB I237.CB -10. 7.0 14.0 0.608 bonus Constraint I132.CB A148.CB -10. 7.0 14.0 0.608 bonus Constraint A131.CB Y149.CB -10. 7.0 14.0 0.608 bonus Constraint S228.CB L245.CB -10. 7.0 14.0 0.605 bonus Constraint L164.CB V208.CB -10. 7.0 14.0 0.605 bonus Constraint T150.CB F239.CB -10. 7.0 14.0 0.605 bonus Constraint G140.CA N151.CB -10. 7.0 14.0 0.605 bonus Constraint I132.CB L235.CB -10. 7.0 14.0 0.605 bonus Constraint F154.CB L235.CB -10. 7.0 14.0 0.602 bonus Constraint F154.CB V208.CB -10. 7.0 14.0 0.602 bonus Constraint A148.CB L247.CB -10. 7.0 14.0 0.602 bonus Constraint I132.CB I153.CB -10. 7.0 14.0 0.602 bonus