//Based on try4.costfcn, but all non-sheet-related constraints are removed, //except for defining helices and a couple of consistently predicted pairings //Jenny, 7-9-04, 8pm CreatePredAlphaCost pred_alpha2k alpha11 T0208.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0208.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 3 \ constraints 10 \ hbond_geom 0.1 \ hbond_geom_backbone 0.1 \ hbond_geom_beta 0.4 \ hbond_geom_beta_pair 1 // 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, // ssbond, hbond, or just arbitrary pairs of atoms. # from try3-opt2 HelixConstraint V44 G58 HelixConstraint D81 G95 HelixConstraint Q139 K152 HelixConstraint Q150 R155 #HelixConstraint P140 R155 #merged HelixConstraint Q166 M173 HelixConstraint T178 E199 HelixConstraint N224 V235 HelixConstraint D256 G265 HelixConstraint A298 G309 HelixConstraint L333 Q354 # from T0208.t04.dssp-ehl2.constraints # (excluding helices already in try3-opt2) HelixConstraint L17 R21 0.6347 StrandConstraint F5 W7 0.6828 StrandConstraint L61 E65 0.6549 StrandConstraint S100 C103 0.645 StrandConstraint K203 H207 0.6662 StrandConstraint I242 F244 0.6575 StrandConstraint F270 F273 0.7972 # try to make a possible strand around 125-130ish StrandConstraint G126 L129 0.65 # keep 28-332 helical HelixConstraint G28 T32 # try to make a ring of nearest-neighbor connections around the barrel # edited from the try4 guess SheetConstraint R315 D317 G4 R6 4 SheetConstraint F5 Y8 L62 E65 3 SheetConstraint L62 E65 V102 S105 5 #SheetConstraint V102 S105 Q150 G153 3 #SheetConstraint S151 R155 K203 H207 3 SheetConstraint V102 S104 G126 L129 3 SheetConstraint G126 L129 K203 H207 3 SheetConstraint K203 H207 A239 T243 4 SheetConstraint I242 T246 N269 F273 4 SheetConstraint F270 F273 V313 P316 4 # from try3-opt2.sheets SheetConstraint F270 F273 V313 P316 hbond V271 #from robetta1.sheets SheetConstraint S100 V102 G124 L126 hbond V102 #ok # SheetConstraint E160 R163 I202 G205 hbond E162 SheetConstraint K203 H207 A239 T243 hbond M204 #ok SheetConstraint T243 C245 F270 H272 hbond F244 #good SheetConstraint V271 F273 I314 P316 hbond V271 #good # mi constraints with weight >0.5 #from t2k-thin30.mi.constraints (only 2 sequences---pretty useless) #from t2k-thin35.mi.constraints (only 4 sequences) #from t2k-thin40.mi.constraints (only 5 sequences) #from t2k-thin50.mi.constraints (only 8 sequences) >=0.6 Constraint E285.CB A327.CB -10. 7.0 12.0 0.687658 #from t2k-thin62.mi.constraints Constraint S66.CB P108.CB -10. 7.0 12.0 0.614792 #this is a common pairing in the constraint files #and in George's rr predictions... lets keep it in #from t04-thin40.mi.constraints Constraint T243.CB H318.CB -10. 7.0 12.0 0.561756 Constraint T243.CB R320.CB -10. 7.0 12.0 0.559147 #from t04-thin50.mi.constraints (>= 0.55) Constraint C245.CB D317.CB -10. 7.0 12.0 0.613951 Constraint N240.CB D317.CB -10. 7.0 12.0 0.556341 #from t04-thin62.mi.constraints (>=0.7) Constraint C245.CB D317.CB -10. 7.0 12.0 1.29809 Constraint C245.CB R274.CB -10. 7.0 12.0 0.804197 Constraint F270.CB R315.CB -10. 7.0 12.0 0.762868 Constraint R274.CB D317.CB -10. 7.0 12.0 0.759125 #from try4-opt2.constraints (The bit of sheet we like) constraint R315.CA D317.CA 6.04 6.54 7.14 1 # cost= -0.7726 dist= 6.43 constraint F189.CB D317.CB -10 7 12 0.706 # cost= 3.339 dist= 21.5 constraint N240.CB D317.CB -10 7 12 0.556 # cost= 2.018 dist= 18.3 constraint R274.CB D317.CB -10 7 12 0.759 # cost= -0.8877 dist= 5.68 constraint C245.CB D317.CB -10 7 12 1.3 # cost= -0.9123 dist= 5.99 constraint C245.CB D317.CB -10 7 12 0.614 # cost= -0.9123 dist= 5.99 constraint S100.CA G124.CA 4.34 4.84 5.34 1 # cost= 4.005 dist= 6.99 constraint L101.N G124.O 2.3 2.87 3.44 0.0333 # cost= 3.818 dist= 5.07 constraint T243.CA F270.CA 4.34 4.84 5.34 1 # cost= -0.8673 dist= 4.91 constraint T243.CA F270.CA 4.34 4.84 5.34 1 # cost= -0.8673 dist= 4.91 constraint T243.CB F270.CB 4.64 5.14 5.64 1 # cost= 0.2016 dist= 4.53 constraint T243.CB F270.CB 4.64 5.14 5.64 1 # cost= 0.2016 dist= 4.53 constraint F244.N F270.O 2.3 2.87 3.44 0.0333 # cost= -0.5117 dist= 3.16 constraint C245.CA H272.CA 4.34 4.84 5.34 1 # cost= 0.3582 dist= 4.15 constraint C245.CA H272.CA 4.34 4.84 5.34 1 # cost= 0.3582 dist= 4.15 constraint C245.CB H272.CB 4.64 5.14 5.64 1 # cost= 1.943 dist= 3.47 constraint C245.CB H272.CB 4.64 5.14 5.64 1 # cost= 1.943 dist= 3.47 constraint T246.CA F273.CA 4.34 4.84 5.34 1 # cost= 1.087 dist= 5.83 constraint V271.CA F273.CA 6.04 6.54 7.14 0.2 # cost= 0.6969 dist= 5.67 constraint V271.CA F273.CA 6.04 6.54 7.14 0.1 # cost= 0.6969 dist= 5.67 constraint V271.CA F273.CA 6.04 6.54 7.14 0.25 # cost= 0.6969 dist= 5.67 constraint V271.CA F273.CA 6.04 6.54 7.14 0.25 # cost= 0.6969 dist= 5.67 constraint V271.CA F273.CA 6.04 6.54 7.14 0.399 # cost= 0.6969 dist= 5.67 constraint N269.CA F273.CA 12.1 13.1 13.7 0.25 # cost= -0.6786 dist= 12.8 constraint T246.CB F273.CB 4.64 5.14 5.64 1 # cost= 1.292 dist= 6.23 constraint D317.N F273.O 2.3 2.87 3.44 0.05 # cost= -0.172 dist= 3.35 constraint D317.N F273.O 2.3 2.87 3.44 0.05 # cost= -0.172 dist= 3.35 constraint I206.CA I242.CA 4.34 4.84 5.34 1 # cost= -0.9195 dist= 4.8 constraint I206.CA I242.CA 4.34 4.84 5.34 1 # cost= -0.9195 dist= 4.8 constraint I206.CB I242.CB 4.64 5.14 5.64 1 # cost= 2.875 dist= 6.88 constraint I206.CB I242.CB 4.64 5.14 5.64 1 # cost= 2.875 dist= 6.88 constraint H207.N I242.O 2.3 2.87 3.44 0.02 # cost= 6.39 dist= 5.92 constraint I242.CA F244.CA 6.04 6.54 7.14 0.25 # cost= 0.1526 dist= 5.96 constraint I242.CA F244.CA 6.04 6.54 7.14 0.658 # cost= 0.1526 dist= 5.96 constraint H272.N F244.O 2.3 2.87 3.44 0.0333 # cost= -0.3554 dist= 2.51 constraint T243.CA C245.CA 6.04 6.54 7.14 0.2 # cost= -0.9879 dist= 6.55 constraint T243.CA C245.CA 6.04 6.54 7.14 0.25 # cost= -0.9879 dist= 6.55 constraint F273.N C245.O 2.3 2.87 3.44 0.0333 # cost= 10.41 dist= 7.04