CreatePredAlphaCost pred_alpha2k alpha11 T0296.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0296.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0296.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 20 backbone_clashes 2 \ break 50 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 10 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ missing_atoms 1 \ maybe_metal 0.5 \ maybe_ssbond 1 // remove maybe_ssbond weight if protein known to be in reducing environment. // remove maybe_metal weight if protein known to have disulfides or // known not to bind metal ions. // Add the following for extra-cellular proteins: # known_ssbond 0.5 # and put ssbond command in constraints file // 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 T0296.dssp-ehl2.constraints HelixConstraint I3 Q16 0.6012 HelixConstraint L29 D31 0.6012 HelixConstraint I37 E65 0.8423 StrandConstraint I70 N72 0.7387 StrandConstraint V75 S76 0.6122 HelixConstraint P79 G84 0.6437 HelixConstraint T90 E105 0.6566 StrandConstraint F110 G112 0.6873 HelixConstraint D126 A138 0.6774 StrandConstraint V143 S145 0.6409 HelixConstraint M158 T171 0.7696 HelixConstraint P216 K225 0.7745 HelixConstraint F231 T241 0.7847 HelixConstraint Q250 R259 0.6678 StrandConstraint K181 F185 0.6588 StrandConstraint V207 N210 0.751 StrandConstraint G265 D268 0.6816 # include T0296.undertaker-align.sheets #sheet constraints from conformation 0 T0296-1i60A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1i60A # SheetConstraint (T0296)T22 (T0296)T24 (T0296)I70 (T0296)N72 hbond (T0296)I23 3.18078 # SheetConstraint (T0296)I70 (T0296)K73 (T0296)D109 (T0296)G112 hbond (T0296)V71 3.18078 # SheetConstraint (T0296)K73 (T0296)V75 (T0296)I27 (T0296)L29 hbond (T0296)R74 3.18078 SheetConstraint (T0296)D109 (T0296)G113 (T0296)K142 (T0296)S146 hbond (T0296)F110 3.18078 # a bulge in the next two?? SheetConstraint (T0296)C144 (T0296)S145 (T0296)V179 (T0296)A180 hbond (T0296)S145 3.18078 SheetConstraint (T0296)S146 (T0296)N148 (T0296)L182 (T0296)V184 hbond (T0296)V147 3.18078 SheetConstraint (T0296)V183 (T0296)F185 (T0296)V267 (T0296)L269 hbond (T0296)F185 3.18078 #sheet constraints from conformation 1 T0296-1qtwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1qtwA # these reinforce the first # SheetConstraint (T0296)P69 (T0296)R74 (T0296)V108 (T0296)G113 hbond (T0296)V71 1.56674 # SheetConstraint (T0296)V71 (T0296)N72 (T0296)D31 (T0296)C32 hbond (T0296)N72 1.56674 SheetConstraint (T0296)D109 (T0296)G113 (T0296)K142 (T0296)S146 hbond (T0296)F110 1.56674 SheetConstraint (T0296)C144 (T0296)S145 (T0296)V179 (T0296)A180 hbond (T0296)S145 1.56674 SheetConstraint (T0296)S146 (T0296)N148 (T0296)L182 (T0296)V184 hbond (T0296)V147 1.56674 #sheet constraints from conformation 2 T0296-1c93A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1c93A # SheetConstraint (T0296)I20 (T0296)I27 (T0296)P69 (T0296)S76 hbond (T0296)R21 1.33659 # SheetConstraint (T0296)V71 (T0296)V75 (T0296)F110 (T0296)F114 hbond (T0296)N72 1.33659 SheetConstraint (T0296)F110 (T0296)F114 (T0296)V143 (T0296)V147 hbond (T0296)I111 1.33659 SheetConstraint (T0296)L182 (T0296)V184 (T0296)D206 (T0296)I208 hbond (T0296)V183 1.33659 SheetConstraint (T0296)L182 (T0296)V184 (T0296)S145 (T0296)V147 hbond (T0296)V184 1.33659 # SheetConstraint (T0296)N210 (T0296)V213 (T0296)F194 (T0296)D191 hbond (T0296)G212 1.33659 #sheet constraints from conformation 3 T0296-1j0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1j0dA # SheetConstraint (T0296)I20 (T0296)G26 (T0296)P69 (T0296)V75 hbond (T0296)R21 1.19477 # SheetConstraint (T0296)I20 (T0296)I23 (T0296)C144 (T0296)V147 hbond (T0296)T22 1.19477 # SheetConstraint (T0296)V71 (T0296)K73 (T0296)D109 (T0296)I111 hbond (T0296)N72 1.19477 SheetConstraint (T0296)K181 (T0296)A186 (T0296)V207 (T0296)G212 hbond (T0296)L182 1.19477 #sheet constraints from conformation 4 T0296-1p1xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1p1xA # SheetConstraint (T0296)T22 (T0296)M25 (T0296)P69 (T0296)N72 hbond (T0296)T24 0.747573 # SheetConstraint (T0296)P69 (T0296)N72 (T0296)V108 (T0296)I111 hbond (T0296)V71 0.747573 SheetConstraint (T0296)I111 (T0296)G113 (T0296)C144 (T0296)S146 hbond (T0296)G112 0.747573 # SheetConstraint (T0296)G112 (T0296)F114 (T0296)S76 (T0296)T78 hbond (T0296)G113 0.747573 SheetConstraint (T0296)M177 (T0296)G178 (T0296)V143 (T0296)C144 hbond (T0296)G178 0.747573 #sheet constraints from conformation 5 T0296-1pdo-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1pdo # SheetConstraint (T0296)I70 (T0296)K73 (T0296)V108 (T0296)I111 hbond (T0296)I70 0.659985 # SheetConstraint (T0296)P69 (T0296)K73 (T0296)S146 (T0296)G150 hbond (T0296)V71 0.659985 SheetConstraint (T0296)A89 (T0296)T90 (T0296)G113 (T0296)G112 hbond (T0296)A89 0.659985 SheetConstraint (T0296)S145 (T0296)S151 (T0296)D206 (T0296)G212 hbond (T0296)S146 0.659985 #sheet constraints from conformation 6 T0296-1z41A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1z41A # SheetConstraint (T0296)I20 (T0296)I23 (T0296)P69 (T0296)N72 hbond (T0296)R21 0.615097 # SheetConstraint (T0296)V71 (T0296)K73 (T0296)F110 (T0296)G112 hbond (T0296)N72 0.615097 SheetConstraint (T0296)I111 (T0296)S115 (T0296)V143 (T0296)V147 hbond (T0296)G113 0.615097 SheetConstraint (T0296)C144 (T0296)I149 (T0296)K181 (T0296)A186 hbond (T0296)S145 0.615097 #sheet constraints from conformation 7 T0296-7odcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:7odcA # SheetConstraint (T0296)V75 (T0296)S76 (T0296)F110 (T0296)I111 hbond (T0296)S76 0.523219 SheetConstraint (T0296)F110 (T0296)G113 (T0296)K142 (T0296)S145 hbond (T0296)I111 0.523219 SheetConstraint (T0296)C144 (T0296)S146 (T0296)V184 (T0296)A186 hbond (T0296)S145 0.523219 SheetConstraint (T0296)G155 (T0296)I156 (T0296)S146 (T0296)V147 hbond (T0296)I156 0.523219 SheetConstraint (T0296)V184 (T0296)A186 (T0296)I266 (T0296)D268 hbond (T0296)F185 0.523219 #sheet constraints from conformation 8 T0296-1e6uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1e6uA # SheetConstraint (T0296)I20 (T0296)I23 (T0296)I70 (T0296)K73 hbond (T0296)R21 0.522145 # SheetConstraint (T0296)I70 (T0296)V75 (T0296)D109 (T0296)F114 hbond (T0296)V71 0.522145 SheetConstraint (T0296)G112 (T0296)S115 (T0296)I208 (T0296)V211 hbond (T0296)F114 0.522145 SheetConstraint (T0296)S146 (T0296)I149 (T0296)G265 (T0296)D268 hbond (T0296)V147 0.522145 #sheet constraints from conformation 9 T0296-1jmvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1jmvA # SheetConstraint (T0296)R21 (T0296)I27 (T0296)N72 (T0296)T78 hbond (T0296)T22 0.46503 SheetConstraint (T0296)F110 (T0296)S115 (T0296)V143 (T0296)N148 hbond (T0296)I111 0.46503 include rr.0.1.constraints