CreatePredAlphaCost pred_alpha2k alpha11 T0283.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0283.t04.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 25 dry8 15 dry12 10 \ phobic_fit 4 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 20 backbone_clashes 2 \ break 60 \ pred_alpha2k 4 \ pred_alpha04 4 \ constraints 10 \ hbond_geom 5 \ hbond_geom_backbone 10 # No reward for beta sheets in THIS protein # hbond_geom_beta 50 \ # hbond_geom_beta_pair 100 # from T0283.dssp-ehl2.constraints # HelixConstraint F3 K25 0.682 # HelixConstraint K29 T44 0.7839 # HelixConstraint W51 A70 0.7193 # HelixConstraint T76 D77 0.6175 # HelixConstraint V83 D93 0.7024 # HelixConstraint M98 L105 0.6139 # split the first helix constraint HelixConstraint F3 L11 07.00 HelixConstraint K14 K25 08.17 # shrink the second helix to higher-confidence region HelixConstraint K29 W43 08.574 HelixConstraint W51 A70 07.193 # eliminate tiny 3-10 helix (V75-D77) # HelixConstraint T76 D77 06.175 # shrink next helix to high-confidence region HelixConstraint V83 K92 08.259 # shrink last helix to high-confidence region HelixConstraint K100 L105 07.202 # 3-10 predictions # from n_notor2 Hbond L27.N A24.O 0.54 Hbond G72.N A69.O 0.49 Hbond G72.N G68.O 0.31 # Hbond S10.N M7.O 0.32 alpha helix stronger # Hbond Y31.N P28.O 0.31 alpha helix stronger # from o_notor2 Hbond A24.O L27.N 0.52 Hbond A69.O G72.N 0.75 Hbond A70.O K73.N 0.34 Hbond M91.O T94.N 0.30 # packing the final helix Constraint L105.CB V83.CB -10. 7.0 14.0 1 Constraint Y101.CB C87.CB -10. 7.0 14.0 1 # Constraints from rr.constraints, selected for conserved residues # that look like they ought to pair Constraint F65.CB F86.CB -10. 7.0 14.0 3 #Constraint L62.CB L90.CB -10. 7.0 14.0 3 this seems too difficult right now #Constraint I61.CB V83.CB -10. 7.0 14.0 0.628027969049 I want to add this next time #from rr.constraints (scaled down by 10) # Constraint L27.CB I38.CB -10. 7.0 14.0 0.0891394 # Constraint A24.CB I38.CB -10. 7.0 14.0 0.0890471 # Constraint M42.CB I57.CB -10. 7.0 14.0 0.0888313 # Constraint L90.CB L105.CB -10. 7.0 14.0 0.0887868 # Constraint I38.CB I57.CB -10. 7.0 14.0 0.088592 # Constraint M42.CB L64.CB -10. 7.0 14.0 0.0885645 # Constraint A24.CB A34.CB -10. 7.0 14.0 0.0885619 # Constraint I38.CB L64.CB -10. 7.0 14.0 0.0883845 # Constraint I38.CB I61.CB -10. 7.0 14.0 0.088353 # Constraint I61.CB V83.CB -10. 7.0 14.0 0.0883291 # Constraint M42.CB I61.CB -10. 7.0 14.0 0.0883266 # Constraint L78.CB L90.CB -10. 7.0 14.0 0.088234 # Constraint F65.CB L90.CB -10. 7.0 14.0 0.0881606 # Constraint A24.CB M42.CB -10. 7.0 14.0 0.0881384 # Constraint I38.CB L62.CB -10. 7.0 14.0 0.0881242 # Constraint L27.CB M42.CB -10. 7.0 14.0 0.0881143 # Constraint I61.CB L78.CB -10. 7.0 14.0 0.0879994 # Constraint M42.CB F65.CB -10. 7.0 14.0 0.0879728 # Constraint F65.CB V83.CB -10. 7.0 14.0 0.0879575 # Constraint I61.CB L90.CB -10. 7.0 14.0 0.0879425 # Constraint M42.CB L62.CB -10. 7.0 14.0 0.0878712 # Constraint V83.CB L105.CB -10. 7.0 14.0 0.0878145 # Constraint C87.CB L105.CB -10. 7.0 14.0 0.0878093 # Constraint M91.CB L105.CB -10. 7.0 14.0 0.0877483 # Constraint A24.CB Y35.CB -10. 7.0 14.0 0.087738 # Constraint L90.CB Y101.CB -10. 7.0 14.0 0.0877338 # Constraint M42.CB T54.CB -10. 7.0 14.0 0.0877242 # Constraint A24.CB L64.CB -10. 7.0 14.0 0.0877189 # Constraint L62.CB L90.CB -10. 7.0 14.0 0.0876761 # Constraint I61.CB A70.CB -10. 7.0 14.0 0.0876512 # Constraint T54.CB L64.CB -10. 7.0 14.0 0.0876474 # Constraint M7.CB I38.CB -10. 7.0 14.0 0.0876457 # Constraint K55.CB L64.CB -10. 7.0 14.0 0.0876345 # Constraint L62.CB V83.CB -10. 7.0 14.0 0.0875805 # Constraint F65.CB F86.CB -10. 7.0 14.0 0.0875476 # Constraint M42.CB F58.CB -10. 7.0 14.0 0.0875369 # Constraint F65.CB L78.CB -10. 7.0 14.0 0.0875098 # Constraint F65.CB V75.CB -10. 7.0 14.0 0.0875068 # Constraint F65.CB C87.CB -10. 7.0 14.0 0.0874337 # Constraint L62.CB L78.CB -10. 7.0 14.0 0.0874056 # Constraint F65.CB L105.CB -10. 7.0 14.0 0.0873885 # Constraint I61.CB L105.CB -10. 7.0 14.0 0.0873628 # Constraint F65.CB M91.CB -10. 7.0 14.0 0.0873581 # Constraint I61.CB M91.CB -10. 7.0 14.0 0.0873543 # Constraint L64.CB L90.CB -10. 7.0 14.0 0.0873471 # Constraint M7.CB M20.CB -10. 7.0 14.0 0.0873003 # Constraint L62.CB M91.CB -10. 7.0 14.0 0.0872979 # Constraint L62.CB L105.CB -10. 7.0 14.0 0.0872455 # Constraint T79.CB L90.CB -10. 7.0 14.0 0.087235 # Constraint A24.CB I57.CB -10. 7.0 14.0 0.0872193 # Constraint F58.CB L90.CB -10. 7.0 14.0 0.08719 # Constraint Q52.CB L64.CB -10. 7.0 14.0 0.0871773 # Constraint L64.CB L78.CB -10. 7.0 14.0 0.0871767 # Constraint M7.CB W17.CB -10. 7.0 14.0 0.087166 # Constraint A24.CB Y41.CB -10. 7.0 14.0 0.0871589 # Constraint L90.CB I109.CB -10. 7.0 14.0 0.0871467 # Constraint I57.CB L78.CB -10. 7.0 14.0 0.0871286 # Constraint I61.CB V75.CB -10. 7.0 14.0 0.0871161 # Constraint L64.CB V83.CB -10. 7.0 14.0 0.0870916 # Constraint C87.CB Y101.CB -10. 7.0 14.0 0.0870639 # Constraint I57.CB L90.CB -10. 7.0 14.0 0.0870447 # Constraint I61.CB F86.CB -10. 7.0 14.0 0.0870299 # Constraint I57.CB V83.CB -10. 7.0 14.0 0.0870289 # Constraint Y35.CB L64.CB -10. 7.0 14.0 0.0870157 # Constraint L64.CB V75.CB -10. 7.0 14.0 0.0869918 # Constraint F58.CB L78.CB -10. 7.0 14.0 0.0869891 # Constraint F86.CB L105.CB -10. 7.0 14.0 0.0869701 # Constraint V75.CB L90.CB -10. 7.0 14.0 0.0869559 # Constraint L62.CB F86.CB -10. 7.0 14.0 0.0869408 # Constraint Y35.CB I57.CB -10. 7.0 14.0 0.0869381 # Constraint L62.CB V75.CB -10. 7.0 14.0 0.0869272 # Constraint M91.CB I109.CB -10. 7.0 14.0 0.0869009 # Constraint M20.CB Y31.CB -10. 7.0 14.0 0.0868958 # Constraint L62.CB C87.CB -10. 7.0 14.0 0.0868813 # Constraint V83.CB I109.CB -10. 7.0 14.0 0.0868756 # Constraint I38.CB L90.CB -10. 7.0 14.0 0.0868602 # Constraint C87.CB W97.CB -10. 7.0 14.0 0.0868239 # Constraint I61.CB C87.CB -10. 7.0 14.0 0.0868223 # Constraint A24.CB I61.CB -10. 7.0 14.0 0.0868161 # Constraint F86.CB W97.CB -10. 7.0 14.0 0.0868056 # Constraint V83.CB W97.CB -10. 7.0 14.0 0.0867983 # Constraint M42.CB W51.CB -10. 7.0 14.0 0.0867925 # Constraint L64.CB F86.CB -10. 7.0 14.0 0.0867835 # Constraint L90.CB R102.CB -10. 7.0 14.0 0.0867642 # Constraint L27.CB L64.CB -10. 7.0 14.0 0.0867578 # Constraint F58.CB V83.CB -10. 7.0 14.0 0.0867408 # Constraint M20.CB I38.CB -10. 7.0 14.0 0.086702 # Constraint F58.CB F86.CB -10. 7.0 14.0 0.0866888 # Constraint I38.CB V83.CB -10. 7.0 14.0 0.0866698 # Constraint I61.CB T79.CB -10. 7.0 14.0 0.0866657 # Constraint L27.CB I57.CB -10. 7.0 14.0 0.0866625 # Constraint L64.CB L105.CB -10. 7.0 14.0 0.0866577 # Constraint M42.CB L78.CB -10. 7.0 14.0 0.0866552 # Constraint W43.CB L64.CB -10. 7.0 14.0 0.0866527 # Constraint G68.CA L78.CB -10. 7.0 14.0 0.0866245 # Constraint L64.CB M91.CB -10. 7.0 14.0 0.0866144 # Constraint Y31.CB M42.CB -10. 7.0 14.0 0.0866125 # Constraint M7.CB L27.CB -10. 7.0 14.0 0.0865972 # Constraint M42.CB V83.CB -10. 7.0 14.0 0.0865933 # Constraint F58.CB V75.CB -10. 7.0 14.0 0.086578 # Constraint M42.CB F86.CB -10. 7.0 14.0 0.0865618 # Constraint F58.CB G68.CA -10. 7.0 14.0 0.0865601 # Constraint F58.CB A70.CB -10. 7.0 14.0 0.0865536 # Constraint I4.CB I38.CB -10. 7.0 14.0 0.0865528 # Constraint T76.CB L90.CB -10. 7.0 14.0 0.0865465 # Constraint I61.CB I109.CB -10. 7.0 14.0 0.0865447 # Constraint F86.CB Y101.CB -10. 7.0 14.0 0.0865348 # Constraint I4.CB L27.CB -10. 7.0 14.0 0.0865292 # Constraint A24.CB Q39.CB -10. 7.0 14.0 0.086517 # Constraint F86.CB I109.CB -10. 7.0 14.0 0.0865078 # Constraint I38.CB F65.CB -10. 7.0 14.0 0.0865071 # Constraint A69.CB L78.CB -10. 7.0 14.0 0.0865021