CreatePredAlphaCost pred_alpha2k alpha11 T0349.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0349.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0349.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 25 dry6.5 33 dry8 23 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 7 bad_peptide 13 \ bystroff 5 \ soft_clashes 50 backbone_clashes 2 \ break 150 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 15 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ missing_atoms 1 \ maybe_metal 0.2 \ maybe_ssbond 0 // 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 T0349.dssp-ehl2.constraints //include T0349.undertaker-align.sheets //include rr.constraints SheetConstraint (T0349)L4 (T0349)T7 (T0349)R47 (T0349)I44 hbond (T0349)L5 1 SheetConstraint (T0349)I25 (T0349)L30 (T0349)V50 (T0349)P45 hbond (T0349)G26 1 //The above line changed from try1 (used to span from I25 to L28 and from V50 to R47) SheetConstraint (T0349)L28 (T0349)V29 (T0349)V48 (T0349)R47 hbond (T0349)V29 1 Constraint L49.CB L61.CB -10. 7.0 14.0 0.672599285153 Constraint L13.CB L41.CB -10. 7.0 14.0 0.6 Constraint L5.CB L30.CB -10. 7.0 14.0 0.554201790573 Constraint L49.CB L67.CB -10. 7.0 14.0 0.492451990664 bonus Constraint L13.CB L41.CB -10. 7.0 14.0 0.490071273609 bonus Constraint L30.CB R46.CB -10. 7.0 14.0 0.460698945128 bonus Constraint L13.CB I44.CB -10. 7.0 14.0 0.459635315989 bonus Constraint L13.CB L62.CB -10. 7.0 14.0 0.444139027593 bonus Constraint V48.CB L61.CB -10. 7.0 14.0 0.425573678469 bonus Constraint L13.CB V48.CB -10. 7.0 14.0 0.422750445492 bonus Constraint L49.CB A58.CB -10. 7.0 14.0 0.381985712286 bonus Constraint V29.CB V43.CB -10. 7.0 14.0 0.374752748988 bonus Constraint L13.CB L61.CB -10. 7.0 14.0 0.372585546559 bonus Constraint L30.CB L49.CB -10. 7.0 14.0 0.363797157143 bonus Constraint L5.CB A15.CB -10. 7.0 14.0 0.363528057143 bonus Constraint V48.CB A58.CB -10. 7.0 14.0 0.363312185714 bonus Constraint L12.CB V48.CB -10. 7.0 14.0 0.360843490411 bonus Constraint I44.CB L61.CB -10. 7.0 14.0 0.356294509874 bonus Constraint G26.CA L55.CB -10. 7.0 14.0 0.355572995425 bonus Constraint V29.CB V48.CB -10. 7.0 14.0 0.355237571821 bonus Constraint L13.CB I25.CB -10. 7.0 14.0 0.353624344007 bonus Constraint S14.CB V48.CB -10. 7.0 14.0 0.352173432052 bonus Constraint L41.CB V50.CB -10. 7.0 14.0 0.351942048735 bonus Constraint V11.CB V48.CB -10. 7.0 14.0 0.346260539901 bonus Constraint A18.CB L62.CB -10. 7.0 14.0 0.345900265025 bonus Constraint V48.CB L62.CB -10. 7.0 14.0 0.338819452983 bonus Constraint V16.CB L61.CB -10. 7.0 14.0 0.334203231733 bonus Constraint L19.CB I36.CB -10. 7.0 14.0 0.331842119388 bonus Constraint L5.CB V16.CB -10. 7.0 14.0 0.330972503061 bonus Constraint L28.CB V48.CB -10. 7.0 14.0 0.323417628664 bonus Constraint V29.CB R47.CB -10. 7.0 14.0 0.320930217934 bonus Constraint V29.CB L49.CB -10. 7.0 14.0 0.305001579327 bonus Constraint L5.CB A18.CB -10. 7.0 14.0 0.303167770254 bonus