CreatePredAlphaCost pred_alpha2k alpha11 T0338.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0338.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0338.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 T0338.dssp-ehl2.constraints #include T0338.undertaker-align.sheets #include rr.constraints Constraint I76.CB M133.CB -10. 7.0 14.0 0.601545537313 Constraint H60.CB S77.CB -10. 7.0 14.0 0.574932381932 Constraint M59.CB L83.CB -10. 7.0 14.0 0.552654894108 Constraint L83.CB M133.CB -10. 7.0 14.0 0.550353958212 Constraint A55.CB S77.CB -10. 7.0 14.0 0.542377608627 Constraint E130.CB F139.CB -10. 7.0 14.0 0.531776376545 Constraint A80.CB M133.CB -10. 7.0 14.0 0.516473237024 Constraint A34.CB M59.CB -10. 7.0 14.0 0.472749905089 bonus Constraint T51.CB S77.CB -10. 7.0 14.0 0.469291899838 bonus Constraint A34.CB S77.CB -10. 7.0 14.0 0.464444817027 bonus Constraint I38.CB I189.CB -10. 7.0 14.0 0.460514438032 bonus Constraint I52.CB S77.CB -10. 7.0 14.0 0.453150434248 bonus Constraint L37.CB S77.CB -10. 7.0 14.0 0.450654161779 bonus Constraint I38.CB L81.CB -10. 7.0 14.0 0.448374954011 bonus Constraint I38.CB I52.CB -10. 7.0 14.0 0.445789167603 bonus Constraint T54.CB S77.CB -10. 7.0 14.0 0.429443548258 bonus Constraint S167.CB A197.CB -10. 7.0 14.0 0.423459299352 bonus Constraint I38.CB T54.CB -10. 7.0 14.0 0.419473554745 bonus Constraint L83.CB I189.CB -10. 7.0 14.0 0.408380868354 bonus Constraint T51.CB S78.CB -10. 7.0 14.0 0.396691435644 bonus Constraint A55.CB S78.CB -10. 7.0 14.0 0.396256620226 bonus Constraint I76.CB L137.CB -10. 7.0 14.0 0.382952601089 bonus Constraint T154.CB M170.CB -10. 7.0 14.0 0.38048287014 bonus #Constraint I38.CB V97.CB -10. 7.0 14.0 0.3799703958 bonus #increase this one to a real constraint, not a bonus to tuck in helix Constraint I38.CB V97.CB -10. 7.0 14.0 0.8 Constraint G42.CA I52.CB -10. 7.0 14.0 0.372502039676 bonus Constraint M41.CB S78.CB -10. 7.0 14.0 0.369532003384 bonus Constraint M41.CB A55.CB -10. 7.0 14.0 0.365701557143 bonus Constraint M59.CB A80.CB -10. 7.0 14.0 0.365184057143 bonus Constraint I52.CB Y63.CB -10. 7.0 14.0 0.365086471429 bonus Constraint A35.CB L45.CB -10. 7.0 14.0 0.357702086176 bonus Constraint R31.CB M41.CB -10. 7.0 14.0 0.356834402154 bonus Constraint T154.CB L163.CB -10. 7.0 14.0 0.353790914913 bonus Constraint R31.CB S77.CB -10. 7.0 14.0 0.346948485082 bonus Constraint F82.CB L126.CB -10. 7.0 14.0 0.345062552709 bonus Constraint S167.CB A190.CB -10. 7.0 14.0 0.343551155665 bonus Constraint G42.CA T54.CB -10. 7.0 14.0 0.340349608955 bonus Constraint F62.CB S77.CB -10. 7.0 14.0 0.336531832985 bonus Constraint I38.CB A55.CB -10. 7.0 14.0 0.335004400835 bonus Constraint A55.CB A80.CB -10. 7.0 14.0 0.329594927869 bonus Constraint I38.CB S78.CB -10. 7.0 14.0 0.3276296 bonus Constraint A84.CB A190.CB -10. 7.0 14.0 0.326197865957 bonus Constraint A84.CB L196.CB -10. 7.0 14.0 0.322326931896 bonus Constraint I38.CB Y58.CB -10. 7.0 14.0 0.322093606129 bonus Constraint A55.CB A84.CB -10. 7.0 14.0 0.318038672606 bonus Constraint T54.CB Y63.CB -10. 7.0 14.0 0.317814734967 bonus Constraint M59.CB S77.CB -10. 7.0 14.0 0.317582799555 bonus Constraint A55.CB T79.CB -10. 7.0 14.0 0.317116262806 bonus Constraint M59.CB L81.CB -10. 7.0 14.0 0.316804349666 bonus Constraint I38.CB M59.CB -10. 7.0 14.0 0.316436452116 bonus Constraint T54.CB I75.CB -10. 7.0 14.0 0.31502946145 bonus Constraint T154.CB S167.CB -10. 7.0 14.0 0.31475156962 bonus Constraint I38.CB V47.CB -10. 7.0 14.0 0.313837139241 bonus Constraint I38.CB L83.CB -10. 7.0 14.0 0.31250275846 bonus Constraint I56.CB S77.CB -10. 7.0 14.0 0.31187565811 bonus Constraint M41.CB S77.CB -10. 7.0 14.0 0.306875238896 bonus Constraint V150.CB S167.CB -10. 7.0 14.0 0.304493062878 bonus Constraint K86.CB E130.CB -10. 7.0 14.0 0.303180110036 bonus Constraint S78.CB M133.CB -10. 7.0 14.0 0.30228891465 bonus #from try1-opt2.helices HelixConstraint (T0338)A1 (T0338)E10 1 HelixConstraint (T0338)T8 (T0338)E13 1 HelixConstraint (T0338)E27 (T0338)N46 1 HelixConstraint (T0338)S48 (T0338)H66 1 HelixConstraint (T0338)N72 (T0338)E88 1 #HelixConstraint (T0338)K93 (T0338)A101 1 #want to make this helix longer HelixConstraint (T0338)L94 (T0338)L105 3 #HelixConstraint (T0338)P107 (T0338)K115 1 #do not want previous helix #HelixConstraint (T0338)E125 (T0338)G138 1 #want to make this helix longer HelixConstraint (T0338)C116 (T0338)L137 3 HelixConstraint (T0338)H145 (T0338)V151 1 HelixConstraint (T0338)D149 (T0338)T154 1 HelixConstraint (T0338)K152 (T0338)R158 1 HelixConstraint (T0338)S160 (T0338)S174 1 HelixConstraint (T0338)K185 (T0338)S201 1 HelixConstraint (T0338)S208 (T0338)W215 1 HelixConstraint (T0338)T223 (T0338)Q236 1 HelixConstraint (T0338)N243 (T0338)N250 1