This is PLOP, version 1-4n What path for the control file? Contents of the control file: load pdb 2igd.pdb helix auto _:25 _:28 _:41 _:46 Parameters chosen for PDB loading: All protein chains will be loaded. Sequence read from ATOM lines. Ions from PDB file IGNORED. PDB file assumed to be experimental data. Waters from PDB file IGNORED. HETATMs from PDB file IGNORED. NO symmetry will be used. Atoms not in PDB file will NOT be optimized. STARTING TO WORK ON FILE plop_job This is X-RAY DATA Temperature information detected: 300.0000000000000 pH information detected. pH = 4.800000000000000 Based on pH, will substitute HIP for HIS. Waters being ignored ... Amino acid sequence: 0 METB THR PRO ALA VAL THR THR TYR LYS LEU 10 VAL ILE ASN GLY LYS THR LEU LYS GLY GLU 20 THR THR THR LYS ALA VAL ASP ALA GLU THR 30 ALA GLU LYS ALA PHE LYS GLN TYR ALA ASN 40 ASP ASN GLY VAL ASP GLY VAL TRP THR TYR 50 ASP ASP ALA THR LYS THR PHE THR VAL THR 60 GLUE Timings for various book-keeping steps: build 0.170 cross 0.000 child 0.000 iper 0.000 rev 0.010 info 0.000 resat 0.000 rank 0.000 covpt 0.000 sparse 0.000 Times for steps in loading structure: Load sequence 0.03 Initialize structure 0.18 Assign coordinates 0.04 Initialize symmetry 0.00 ========================================== perform helix grid sampling ========================================== Nonbonded initialization ... Time for loading nb parameters: 3.9999999105930328E-002 Time for assigning nb parameters: 9.9999997764825821E-003 Number of chains 1 Number of residues 61 (charged) 16 (polar) 22 (glycine) 4 (hydrophobic) 19 Number of atoms 943 [sparse atoms] 77 Number of bonds 950 Number of angles 1704 Number of torsions 2674 Number of 1/4s 2469 Number of waters 0 Number of ions 0 Number of HET 0 Partial charges and molecular weights: Protein chain -2.0 6648.4 Entire system -2.0 6648.4 Time for dynamic memory allocation: 0.000000000000000 Time for secondary sructure initialization: 0.000000000000000 Preparing for first energy calculation ... Results of parameter assignment type tot exact high med low time BOND 950 715 219 16 0 0.00 ANGL 1704 1030 658 0 16 0.02 TORS 2674 1453 1189 0 32 0.05 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 100.590225 113.158117 149.298961 363.047303 SGB 6325.946341 -2785.705240 -2392.792492 1147.448610 TOTAL 6426.536566 -2672.547123 -2243.493530 1510.495913 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 374.884189 -383.268844 -12.579220 -20.963875 EL 2050.167088 -4534.693897 122.064482 -2362.462327 SGB -2392.792492 3058.018055 -134.636320 530.589243 TOTAL 32.258785 -1859.944686 -25.151058 -1852.836959 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4953.116591 NONPOLAR 25.092294 SGB TOT -882.286247 SOLV TOT -857.193953 TOTALE -2877.572852 WARNING: large bond energies found: 558 552 _:LYS_36:CG 555 _:LYS_36:CD 5.02 Here are the parameters that will be used: Solvent model SGB SGB correction terms INCLUDED Nonpolar estimator SGB/NP Penalty terms INCLUDED Internal dielectric 1.00 Solvent dielectric 80.00 Short NB cut (neutral/neutral) 10.00 Long NB cut (neutral/neutral) 15.00 Short NB cut (charge/neutral) 10.00 Long NB cut (charge/neutral) 20.00 Short NB cut (charge/charge) 15.00 Long NB cut (charge/charge) 30.00 Time for covalent parameter loading: 0.31 Time for contact parameter loading: 0.00 Time for sgb parameter loading: 0.01 Time for dynamic memory allocation: 0.00 Time for covalent parameter assignment: 0.13 Time for nobonded list initialization: 0.02 Time for covalent list initialization: 0.00 Time for sgb initialization: 1.62 ------------------------------------------ Here is a summary of the helix parameters: Helix to be predicted: _:ALA_28 _:ASP_41 Maximum helix endpoint movement (N side): 5.000000000000000 Maximum helix endpoint movement (C side): 5.000000000000000 Helix conformations will NOT be clustered. Only hydrophobic residues will be used in contact energy Will use yaw/pitch/roll angle representation. --------------------------------------------- Helix coordinates: _:ALA_28 _:ASP_41 Axis(z) -0.37 0.92 0.12 Axis(x) 0.84 0.27 0.47 Axis(y) 0.40 0.28 -0.87 Start 11.22 19.47 9.57 Mid 7.68 28.29 10.73 End 4.14 37.11 11.90 RMS = 2.337028164619541 ============================================ Now working on new helix ... Helix: _:ALA_28 _:ASP_41 Total: _:ALA_25 _:GLY_46 ============================================ H-bond contacts in current structure: INTRA HBOND (side/side) _:ASP_27:OD1 _:THR_30:OG1 1 2.748 INTRA HBOND (side/main) _:ASP_27:OD1 _:THR_30:N 1 2.903 [No apparent H-bonds] _:ASP_27:OD2 [No apparent H-bonds] _:GLU_29:OE1 [No apparent H-bonds] _:GLU_29:OE2 INTRA HBOND (side/side) _:THR_30:OG1 _:ASP_27:OD1 1 2.748 [No apparent H-bonds] _:GLU_32:OE1 [No apparent H-bonds] _:GLU_32:OE2 [No apparent H-bonds] _:LYS_33:NZ [No apparent H-bonds] _:LYS_36:NZ [No apparent H-bonds] _:GLN_37:OE1 INTRA HBOND (side/side) _:GLN_37:NE2 _:ASP_41:OD1 1 2.861 [No apparent H-bonds] _:TYR_38:OH [No apparent H-bonds] _:ASN_40:OD1 [No apparent H-bonds] _:ASN_40:ND2 INTRA HBOND (side/side) _:ASP_41:OD1 _:GLN_37:NE2 1 2.861 [No apparent H-bonds] _:ASP_41:OD2 [No apparent H-bonds] _:ASN_42:OD1 INTRA HBOND (side/main) _:ASN_42:ND2 _:TYR_38:O 1 2.942 [No apparent H-bonds] _:ASP_45:OD1 [No apparent H-bonds] _:ASP_45:OD2 Minimum overlap factors for free atoms: (only those with ofac < 1 shown) _:ALA_25:N _:THR_6:O 1 0.98 _:ALA_25:HA _:LYS_24:O 1 0.91 _:ALA_25:C _:ASP_27:N 1 0.94 _:ALA_25:O _:VAL_26:HA 1 0.94 _:VAL_26:N _:VAL_26:HG23 1 0.94 _:VAL_26:HA _:ALA_25:O 1 0.94 _:VAL_26:C _:VAL_26:HG21 1 0.88 * _:VAL_26:O _:ASP_27:HA 1 0.92 _:ASP_27:N _:ALA_25:C 1 0.94 _:ASP_27:HA _:VAL_26:O 1 0.92 _:ASP_27:CB _:VAL_26:O 1 1.00 _:ASP_27:C _:ASP_27:OD1 1 0.85 ** _:ASP_27:O _:ALA_28:C 1 0.91 _:ALA_28:N _:ASP_27:HB1 1 0.96 _:ALA_28:HA _:ASP_27:O 1 0.96 _:ALA_28:C _:ASP_27:O 1 0.91 _:ALA_28:O _:GLU_29:C 1 0.88 * _:GLU_29:N _:ASP_27:C 1 0.95 _:GLU_29:HA _:ALA_28:O 1 0.98 _:GLU_29:C _:GLU_29:HG1 1 0.82 ** _:GLU_29:O _:THR_30:C 1 0.90 * _:THR_30:N _:ALA_28:C 1 0.93 _:THR_30:HA _:GLU_29:O 1 0.95 _:THR_30:C _:THR_30:HG23 1 0.84 ** _:THR_30:O _:ALA_31:C 1 0.88 * _:ALA_31:N _:GLU_29:C 1 0.95 _:ALA_31:HA _:THR_30:O 1 0.97 _:ALA_31:C _:THR_30:O 1 0.88 * _:ALA_31:O _:GLU_32:C 1 0.86 * _:GLU_32:N _:ALA_28:O 1 0.91 _:GLU_32:HA _:ALA_31:O 1 1.00 _:GLU_32:C _:GLU_32:HG1 1 0.85 ** _:GLU_32:O _:LYS_33:C 1 0.87 * _:LYS_33:N _:ALA_31:C 1 0.93 _:LYS_33:HA _:GLU_32:O 1 0.97 _:LYS_33:C _:GLU_32:O 1 0.87 * _:LYS_33:O _:ALA_34:C 1 0.88 * _:ALA_34:N _:GLU_32:C 1 0.94 _:ALA_34:HA _:LYS_33:O 1 0.98 _:ALA_34:C _:LYS_33:O 1 0.88 * _:ALA_34:O _:PHE_35:C 1 0.92 _:PHE_35:N _:ALA_31:O 1 0.95 _:PHE_35:CA _:PHE_35:HD1 1 0.92 _:PHE_35:HA _:PHE_35:HD1 1 0.83 ** _:PHE_35:C _:ALA_34:O 1 0.92 _:PHE_35:O _:LYS_36:C 1 0.89 * _:LYS_36:N _:GLU_32:O 1 0.92 _:LYS_36:HA _:LYS_36:HG2 1 0.90 _:LYS_36:C _:PHE_35:O 1 0.89 * _:LYS_36:O _:GLN_37:C 1 0.89 * _:GLN_37:N _:PHE_35:C 1 0.93 _:GLN_37:HA _:GLN_37:CD 1 0.87 * _:GLN_37:C _:GLN_37:HG2 1 0.83 ** _:GLN_37:O _:TYR_38:C 1 0.86 * _:TYR_38:N _:LYS_36:C 1 0.95 _:TYR_38:C _:GLN_37:O 1 0.86 * _:TYR_38:O _:ALA_39:C 1 0.87 * _:ALA_39:N _:GLN_37:C 1 0.94 _:ALA_39:HA _:TYR_38:O 1 0.98 _:ALA_39:CB _:TRP_48:HZ2 1 0.96 _:ALA_39:C _:TYR_38:O 1 0.87 * _:ALA_39:O _:ASN_40:C 1 0.87 * _:ASN_40:N _:TYR_38:C 1 0.95 _:ASN_40:HA _:ASN_40:ND2 1 0.97 _:ASN_40:C _:ALA_39:O 1 0.87 * _:ASN_40:O _:ASP_41:C 1 0.89 * _:ASP_41:N _:GLN_37:O 1 0.91 _:ASP_41:HA _:ASP_41:OD1 1 0.94 _:ASP_41:C _:ASN_40:O 1 0.89 * _:ASP_41:O _:ASN_42:HA 1 0.89 * _:ASN_42:N _:ASN_40:C 1 0.89 * _:ASN_42:HA _:ASP_41:O 1 0.89 * _:ASN_42:CB _:LEU_17:HD23 1 1.00 _:ASN_42:C _:VAL_44:N 1 0.96 _:ASN_42:O _:ASN_42:HB2 1 0.93 _:GLY_43:N _:ALA_39:O 1 0.99 _:GLY_43:HA2 _:ASN_42:O 1 0.94 _:GLY_43:C _:ASN_42:O 1 0.94 _:GLY_43:O _:VAL_44:HA 1 0.89 * _:VAL_44:N _:VAL_44:HG21 1 0.90 * _:VAL_44:HA _:GLY_43:O 1 0.89 * _:VAL_44:C _:VAL_44:HG13 1 0.81 ** _:VAL_44:O _:ASP_45:HA 1 0.89 * _:ASP_45:N _:GLU_61:OE2 1 0.95 _:ASP_45:HA _:VAL_44:O 1 0.89 * _:ASP_45:C _:ASP_45:OD1 1 0.93 _:ASP_45:O _:GLY_46:HA1 1 0.85 * _:GLY_46:CA _:THR_60:O 1 0.99 _:GLY_46:HA2 _:THR_60:O 1 0.92 _:GLY_46:HA1 _:ASP_45:O 1 0.85 * _:GLY_46:O _:VAL_47:HA 1 0.87 * Side chains to be optimized on body of protein: N-terminal loop length: 10.82000000000000 number of grid points: 11 C-terminal loop length: 17.19000000000000 number of grid points: 18 Summary of contact parameter assignments: RES HELIX SHEET COIL UNK 0 ALA 4 1 2 ARG 0 0 0 ASN 1 1 1 ASP 1 1 3 CYS 0 0 0 GLN 1 0 0 GLU 2 1 1 GLY 0 1 3 HIS 0 0 0 ILE 0 1 0 LEU 0 1 1 LYS 2 3 2 MET 0 0 1 PHE 1 1 0 PRO 0 0 1 SER 0 0 0 THR 1 8 4 TRP 0 1 0 TYR 1 2 0 VAL 0 3 3 Testing starting configuration: Passed N-side loop distance screen: 7.13 10.82 -3 Passed C-side loop distance screen: 13.08 17.18 5 Passed steric clash screen ... Passed side chain screen ... ------------------------------------------------- Determine the helices and strands in the protein ------------------------------------------------- Helices found: 1 4 _:ALA_28 _:ASP_41 14 Strands found: 1 _:THR_6 _:ASN_13 8 2 _:LYS_18 _:ALA_25 8 3 _:VAL_47 _:ASP_51 5 4 _:THR_56 _:VAL_59 4 probing helix: 28 - 41 ================================================== Start evaluating the patch-based contact potential ================================================== HELIX #: 1 : 3 patches STRAND #: 1 : 0 patches Warning: this ss unit has no patches STRAND #: 2 : 0 patches Warning: this ss unit has no patches STRAND #: 3 : 0 patches Warning: this ss unit has no patches STRAND #: 4 : 2 patches ---Total number of patches:= 5 ================================================= Patch Contact Score report: ================================================= total score: -8.070 unmatched score: 0.500 0 0.00 0.00 0.00 0.0 0.0 0.0 -16.96 0.00 0.00 0.00 0.00 length of helix: 19.15851857128381 [dist_min,distmax]: 18.96693338557097 19.35010375699665 Number of roll moves: 1 Number of grid points on the left branch: 479 Number of grid points on the right branch: 513 ================================================== Total number of candidate moves: 245727 ================================================== 1 0.06 -0.76 0.17 -0.2 0.1 0.0 -15.15 1.33 1.37 1.00 1.03 2 -0.13 -0.34 0.37 -0.3 0.1 0.0 -15.21 1.47 1.54 1.18 1.21 3 0.98 -0.49 0.45 -0.2 0.1 0.0 -15.22 1.52 1.57 1.08 1.09 4 0.79 -0.07 0.65 -0.3 0.1 0.0 -15.45 1.64 1.73 1.25 1.26 5 1.04 -0.25 0.01 -0.2 0.1 0.0 -16.41 1.38 1.46 0.99 1.04 6 0.85 0.17 0.21 -0.3 0.2 0.0 -17.34 1.50 1.61 1.16 1.20 7 2.18 -2.02 -0.22 0.0 0.0 0.0 -8.13 2.39 2.48 1.37 1.37 8 2.05 -1.37 -0.46 -0.1 0.0 0.0 -15.33 2.09 2.17 1.18 1.19 9 2.15 -0.39 0.08 -0.2 0.1 0.0 -18.59 1.94 2.02 1.20 1.22 10 3.16 -1.51 -0.38 0.0 0.0 0.0 -10.71 2.81 2.92 1.64 1.65 11 3.22 -1.28 -0.82 0.0 0.0 0.0 -19.32 2.85 2.96 1.65 1.65 12 3.22 -1.28 -0.82 0.0 0.1 0.0 -14.37 2.84 2.95 1.68 1.71 13 3.28 -1.04 -1.25 0.0 0.0 0.0 -21.41 2.92 3.03 1.70 1.73 14 4.20 -0.77 -0.98 0.0 0.1 0.0 -18.64 3.50 3.65 2.09 2.14 15 -1.23 -0.20 0.29 -0.2 0.1 0.0 -16.87 1.55 1.62 1.17 1.18 16 -0.28 -1.55 0.27 -0.1 0.0 0.0 -11.46 1.40 1.45 0.83 0.84 17 -0.40 -0.90 0.03 -0.2 -0.1 0.0 -14.69 1.20 1.28 0.83 0.86 18 -0.53 -0.24 -0.21 -0.3 -0.1 0.0 -15.38 1.34 1.48 1.06 1.10 19 -0.31 0.08 0.57 -0.2 0.1 0.0 -14.65 1.28 1.36 1.04 1.05 20 -0.07 -0.10 -0.07 -0.2 0.1 0.0 -16.19 0.85 0.91 0.70 0.75 21 -0.25 0.31 0.13 -0.2 0.1 0.0 -16.27 1.13 1.23 0.94 0.97 22 0.36 -0.70 -0.91 -0.2 -0.2 0.0 -18.42 1.34 1.54 0.83 0.90 23 0.64 -1.28 0.54 -0.1 0.0 0.0 -11.06 1.35 1.40 0.80 0.80 24 0.70 -1.04 0.11 -0.1 -0.1 0.0 -13.68 1.23 1.31 0.73 0.76 25 0.52 -0.62 0.31 -0.2 -0.1 0.0 -14.10 1.15 1.23 0.79 0.82 26 0.39 0.03 0.07 -0.3 -0.1 0.0 -15.75 1.29 1.43 1.03 1.07 27 0.76 -0.80 -0.33 -0.1 0.0 0.0 -15.97 1.09 1.14 0.64 0.66 28 0.64 -0.15 -0.57 -0.2 -0.1 0.0 -18.79 1.15 1.24 0.80 0.83 29 0.61 0.35 0.85 -0.2 0.1 0.0 -15.59 1.48 1.57 1.11 1.11 30 0.85 0.17 0.21 -0.2 0.1 0.0 -17.41 1.11 1.19 0.81 0.83 31 0.67 0.59 0.41 -0.2 0.1 0.0 -17.65 1.34 1.45 1.03 1.03 32 1.78 -1.92 -0.80 0.0 -0.1 0.0 -12.63 2.21 2.32 1.28 1.27 33 1.81 -1.19 0.18 0.0 0.0 0.0 -12.22 1.75 1.81 1.01 1.00 34 1.87 -0.95 -0.26 0.0 0.0 0.0 -15.67 1.69 1.75 0.98 1.00 35 1.78 0.44 0.49 -0.2 0.1 0.0 -21.17 1.74 1.84 1.13 1.12 36 2.64 -1.89 -0.08 0.1 -0.1 0.0 -9.54 2.61 2.73 1.57 1.54 37 2.70 -1.65 -0.52 0.0 -0.1 0.0 -13.87 2.58 2.70 1.51 1.49 38 2.70 -1.65 -0.52 0.1 0.0 0.0 -11.73 2.59 2.70 1.58 1.57 39 2.76 -1.41 -0.96 0.1 -0.1 0.0 -17.84 2.61 2.72 1.55 1.54 40 2.79 -0.68 0.02 0.0 0.0 0.0 -17.76 2.29 2.38 1.35 1.34 41 2.82 -1.18 -1.39 0.1 0.0 0.0 -20.12 2.71 2.82 1.63 1.64 42 2.85 -0.44 -0.41 0.0 0.1 0.0 -21.96 2.33 2.43 1.39 1.41 43 2.91 -0.20 -0.85 0.0 0.1 0.0 -24.35 2.43 2.56 1.47 1.53 44 3.68 -1.14 -0.68 0.1 -0.1 0.0 -18.43 3.14 3.27 1.87 1.85 45 3.74 -0.90 -1.11 0.1 0.0 0.0 -19.41 3.22 3.35 1.94 1.93 46 -1.57 -0.99 0.39 -0.1 0.0 0.0 -14.60 1.61 1.68 1.02 1.01 47 -1.51 -0.75 -0.05 -0.1 -0.1 0.0 -15.12 1.51 1.60 0.98 0.99 48 -1.69 -0.33 0.16 -0.2 -0.1 0.0 -16.03 1.64 1.74 1.13 1.14 49 -1.48 -0.01 0.93 -0.2 0.1 0.0 -14.89 1.62 1.71 1.11 1.10 50 -1.42 0.22 0.49 -0.1 0.2 0.0 -16.74 1.42 1.54 0.98 0.99 51 -1.36 0.46 0.06 -0.2 0.1 0.0 -18.03 1.41 1.51 1.02 1.02 52 -0.65 -0.71 0.67 -0.1 0.0 0.0 -13.14 1.09 1.14 0.71 0.72 53 -0.59 -0.48 0.23 -0.1 -0.1 0.0 -13.81 0.93 1.02 0.66 0.70 54 -0.77 -0.06 0.43 -0.2 -0.1 0.0 -13.81 1.14 1.24 0.88 0.91 55 -0.40 -0.90 0.03 0.0 0.0 0.0 -14.42 0.81 0.84 0.48 0.48 56 -0.53 -0.24 -0.21 -0.1 0.0 0.0 -15.47 0.74 0.79 0.54 0.55 57 -0.44 0.73 0.34 -0.2 0.1 0.0 -16.72 1.12 1.22 0.87 0.87 58 0.37 -1.83 0.20 0.0 -0.1 0.0 -9.32 1.53 1.64 0.92 0.91 59 0.24 -1.18 -0.03 0.0 -0.1 0.0 -13.08 1.02 1.14 0.56 0.60 60 0.12 -0.52 -0.27 -0.1 -0.2 0.0 -16.22 0.76 0.95 0.48 0.58 61 0.18 -0.29 -0.70 -0.1 -0.2 0.0 -19.44 0.95 1.19 0.62 0.73 62 0.27 -0.44 0.94 -0.1 0.0 0.0 -13.14 1.03 1.08 0.66 0.68 63 0.33 -0.20 0.51 -0.1 -0.1 0.0 -15.14 0.85 0.95 0.61 0.66 64 0.15 0.22 0.71 -0.2 -0.1 0.0 -15.16 1.08 1.18 0.83 0.87 65 0.52 -0.62 0.31 0.0 0.0 0.0 -14.62 0.73 0.75 0.42 0.42 66 0.39 0.03 0.07 -0.1 0.0 0.0 -17.07 0.65 0.70 0.48 0.50 67 0.46 0.27 -0.36 -0.1 -0.1 0.0 -18.91 0.85 0.95 0.63 0.65 68 0.27 0.69 -0.16 -0.2 -0.1 0.0 -18.62 1.08 1.19 0.86 0.87 69 0.58 -0.39 -0.13 0.0 0.0 0.0 -16.52 0.57 0.60 0.34 0.36 70 0.49 1.01 0.61 -0.2 0.1 0.0 -18.47 1.33 1.44 0.95 0.94 71 1.07 -1.88 -0.30 0.1 -0.2 0.0 -11.51 1.82 1.98 1.10 1.10 72 1.29 -1.56 0.48 0.0 -0.1 0.0 -8.75 1.68 1.79 1.01 1.00 73 1.16 -0.90 0.24 0.0 -0.1 0.0 -15.38 1.23 1.35 0.70 0.73 74 1.04 -0.25 0.01 -0.1 -0.2 0.0 -18.55 1.03 1.20 0.64 0.71 75 1.25 0.07 0.78 -0.1 -0.1 0.0 -17.37 1.37 1.46 0.87 0.90 76 1.07 0.49 0.99 -0.2 -0.1 0.0 -17.52 1.52 1.63 1.04 1.06 77 1.35 -1.32 0.04 0.1 -0.1 0.0 -11.49 1.54 1.62 0.95 0.93 78 1.44 -0.35 0.58 0.0 0.0 0.0 -16.06 1.29 1.34 0.76 0.74 79 1.32 0.31 0.35 -0.1 0.0 0.0 -19.91 1.25 1.31 0.79 0.79 80 1.41 -1.09 -0.39 0.1 0.0 0.0 -14.21 1.51 1.58 0.96 0.95 81 1.50 -0.11 0.15 0.0 0.0 0.0 -20.92 1.21 1.26 0.72 0.71 82 1.99 -1.60 -0.02 0.1 -0.2 0.0 -13.23 2.10 2.26 1.28 1.27 83 2.18 -2.02 -0.22 0.2 -0.1 0.0 -11.25 2.52 2.67 1.63 1.60 84 2.27 -1.05 0.32 0.1 -0.1 0.0 -13.37 2.03 2.13 1.24 1.22 85 2.33 -0.81 -0.12 0.0 -0.1 0.0 -18.30 1.99 2.09 1.19 1.17 86 2.24 -1.79 -0.66 0.2 -0.1 0.0 -13.29 2.52 2.66 1.66 1.64 87 2.30 -1.55 -1.09 0.2 -0.1 0.0 -16.98 2.52 2.66 1.61 1.58 88 2.33 -0.81 -0.12 0.1 0.0 0.0 -16.50 2.01 2.10 1.25 1.23 89 3.22 -1.28 -0.82 0.2 -0.1 0.0 -17.89 2.95 3.10 1.86 1.83 90 3.28 -1.04 -1.25 0.2 -0.1 0.0 -19.11 3.06 3.20 1.95 1.93 91 4.20 -0.77 -0.98 0.2 -0.1 0.0 -20.89 3.61 3.77 2.27 2.24 92 -1.85 -1.54 0.05 0.0 -0.1 0.0 -13.62 1.95 2.05 1.17 1.15 93 -1.69 -0.33 0.16 0.0 0.0 0.0 -14.80 1.40 1.45 0.85 0.84 94 -0.92 -1.27 0.33 0.0 -0.1 0.0 -12.05 1.31 1.41 0.80 0.80 95 -1.05 -0.61 0.09 0.0 -0.1 0.0 -13.92 1.01 1.13 0.62 0.67 96 -1.02 0.12 1.07 -0.1 0.0 0.0 -13.14 1.30 1.37 0.86 0.89 97 -0.96 0.36 0.63 -0.1 -0.1 0.0 -13.14 1.16 1.26 0.84 0.89 98 -1.14 0.78 0.83 -0.2 -0.1 0.0 -13.14 1.55 1.67 1.12 1.16 99 -0.86 -1.03 -0.11 0.1 -0.1 0.0 -13.34 1.13 1.19 0.70 0.68 100 -0.80 -0.80 -0.54 0.0 -0.1 0.0 -16.10 1.04 1.13 0.62 0.62 101 -0.77 -0.06 0.43 0.0 0.0 0.0 -13.73 0.74 0.77 0.46 0.47 102 -0.90 0.60 0.20 -0.1 0.0 0.0 -16.16 1.02 1.10 0.73 0.75 103 -0.71 0.18 0.00 0.0 0.0 0.0 -16.99 0.60 0.63 0.37 0.36 104 -0.65 0.41 -0.44 0.0 0.0 0.0 -18.92 0.74 0.77 0.47 0.46 105 -0.22 -1.31 -0.17 0.1 -0.2 0.0 -12.97 1.19 1.36 0.75 0.79 106 0.00 -1.00 0.60 0.0 -0.1 0.0 -12.46 0.97 1.06 0.61 0.63 107 -0.13 -0.34 0.37 0.0 -0.1 0.0 -15.21 0.49 0.66 0.33 0.44 108 -0.25 0.31 0.13 -0.1 -0.2 0.0 -16.41 0.64 0.85 0.53 0.66 109 -0.04 0.63 0.91 -0.1 -0.1 0.0 -16.02 1.10 1.21 0.79 0.85 110 0.06 -0.76 0.17 0.1 -0.1 0.0 -13.38 0.70 0.76 0.48 0.47 111 0.12 -0.52 -0.27 0.0 -0.1 0.0 -16.78 0.55 0.64 0.35 0.37 112 -0.01 0.13 -0.50 0.0 -0.1 0.0 -19.36 0.49 0.64 0.32 0.40 113 0.15 0.22 0.71 0.0 0.0 0.0 -16.05 0.64 0.67 0.39 0.40 114 0.02 0.87 0.47 -0.1 0.0 0.0 -17.33 0.96 1.03 0.69 0.71 115 0.12 -0.52 -0.27 0.1 0.0 0.0 -15.80 0.64 0.68 0.47 0.47 116 0.21 0.45 0.27 0.0 0.0 0.0 -18.08 0.47 0.51 0.28 0.28 117 0.27 0.69 -0.16 0.0 0.0 0.0 -19.84 0.64 0.67 0.42 0.40 118 0.27 0.69 -0.16 0.0 0.1 0.0 -21.21 0.63 0.71 0.38 0.41 119 0.55 -2.25 0.00 0.2 -0.2 0.0 -10.05 2.13 2.32 1.46 1.44 120 0.70 -1.04 0.11 0.1 -0.2 0.0 -14.87 1.12 1.29 0.73 0.78 121 0.92 -0.72 0.88 0.0 -0.1 0.0 -12.52 1.19 1.28 0.74 0.76 122 0.79 -0.07 0.65 0.0 -0.1 0.0 -17.30 0.86 0.98 0.53 0.61 123 0.67 0.59 0.41 -0.1 -0.2 0.0 -18.78 0.95 1.12 0.67 0.79 124 0.89 -1.46 -0.10 0.2 -0.1 0.0 -12.38 1.60 1.72 1.12 1.10 125 0.98 -0.49 0.45 0.1 -0.1 0.0 -15.91 0.99 1.05 0.64 0.64 126 1.04 -0.25 0.01 0.0 -0.1 0.0 -19.36 0.89 0.96 0.55 0.57 127 1.07 0.49 0.99 0.0 0.0 0.0 -18.23 1.24 1.29 0.74 0.73 128 0.95 -1.22 -0.53 0.2 -0.1 0.0 -14.67 1.60 1.71 1.16 1.14 129 1.04 -0.25 0.01 0.1 0.0 0.0 -19.19 0.94 0.99 0.65 0.64 130 1.13 0.73 0.55 0.0 0.0 0.0 -22.02 1.17 1.22 0.69 0.67 131 1.62 -0.77 0.38 0.1 -0.2 0.0 -16.25 1.54 1.69 0.97 1.01 132 1.59 -1.51 -0.59 0.2 -0.2 0.0 -17.74 2.09 2.26 1.43 1.42 133 1.81 -1.19 0.18 0.2 -0.1 0.0 -14.03 1.91 2.04 1.30 1.28 134 1.87 -0.95 -0.26 0.2 -0.1 0.0 -17.32 1.92 2.03 1.34 1.32 135 1.96 0.02 0.29 0.1 0.0 0.0 -20.92 1.63 1.70 1.03 1.01 136 1.93 -0.71 -0.69 0.2 0.0 0.0 -19.38 2.01 2.13 1.42 1.42 137 1.99 -0.48 -1.13 0.2 0.0 0.0 -21.82 2.19 2.32 1.55 1.57 138 2.52 -1.23 -0.32 0.2 -0.2 0.0 -17.63 2.47 2.64 1.65 1.63 139 2.79 -0.68 0.02 0.2 -0.1 0.0 -17.47 2.46 2.59 1.64 1.61 140 2.85 -0.44 -0.41 0.2 0.0 0.0 -19.67 2.54 2.67 1.71 1.69 141 3.50 -0.72 -0.48 0.2 -0.2 0.0 -18.60 3.08 3.24 2.02 1.99 142 3.56 -0.48 -0.91 0.2 -0.2 0.0 -23.45 3.12 3.28 2.00 1.98 143 3.77 -0.17 -0.14 0.2 -0.1 0.0 -20.29 3.11 3.25 1.97 1.93 144 3.62 -0.25 -1.35 0.2 -0.2 0.0 -25.64 3.28 3.43 2.12 2.09 145 3.77 -0.17 -0.14 0.2 0.0 0.0 -18.92 3.18 3.32 2.07 2.04 146 3.83 0.07 -0.57 0.2 -0.1 0.0 -21.84 3.22 3.36 2.05 2.02 147 3.83 0.07 -0.57 0.2 0.0 0.0 -21.15 3.29 3.45 2.16 2.15 148 -2.31 0.69 1.20 -0.1 0.0 0.0 -12.83 2.20 2.31 1.38 1.40 149 -1.66 -1.96 -0.15 0.2 -0.2 0.0 -11.75 2.32 2.49 1.51 1.50 150 -1.29 -0.43 0.73 0.0 -0.1 0.0 -12.65 1.26 1.34 0.77 0.81 151 -1.42 0.22 0.49 0.0 -0.1 0.0 -13.63 1.23 1.34 0.77 0.85 152 -1.39 0.96 1.47 -0.1 0.0 0.0 -13.14 1.86 1.95 1.17 1.22 153 -1.33 1.20 1.04 -0.1 -0.1 0.0 -13.14 1.76 1.88 1.17 1.23 154 -1.23 -0.20 0.29 0.1 -0.1 0.0 -14.62 1.07 1.12 0.65 0.66 155 -1.14 0.78 0.83 0.0 0.0 0.0 -14.71 1.30 1.36 0.78 0.80 156 -1.27 1.43 0.60 -0.1 0.0 0.0 -15.74 1.68 1.77 1.09 1.12 157 -1.08 1.02 0.40 0.0 0.0 0.0 -17.44 1.23 1.29 0.72 0.72 158 -0.92 -1.27 0.33 0.1 -0.3 0.0 -12.41 1.47 1.71 0.97 1.08 159 -0.71 -0.95 1.10 0.1 -0.2 0.0 -11.27 1.38 1.54 0.89 0.97 160 -0.74 0.68 1.41 -0.1 -0.2 0.0 -14.38 1.47 1.62 0.97 1.12 161 -0.74 -1.69 0.13 0.2 -0.2 0.0 -11.41 1.82 1.99 1.27 1.28 162 -0.59 -0.48 0.23 0.1 -0.2 0.0 -14.93 0.79 0.96 0.55 0.67 163 -0.37 -0.16 1.01 0.0 -0.1 0.0 -14.27 0.89 0.97 0.56 0.64 164 -0.47 1.24 1.75 -0.1 0.0 0.0 -15.43 1.82 1.92 1.13 1.19 165 -0.68 -1.45 -0.31 0.2 -0.2 0.0 -12.64 1.75 1.89 1.25 1.25 166 -0.62 -1.22 -0.75 0.2 -0.2 0.0 -14.60 1.64 1.78 1.14 1.15 167 -0.40 -0.90 0.03 0.2 -0.1 0.0 -13.34 1.15 1.25 0.86 0.86 168 -0.31 0.08 0.57 0.1 -0.1 0.0 -16.22 0.61 0.64 0.39 0.44 169 -0.25 0.31 0.13 0.0 -0.1 0.0 -17.54 0.40 0.48 0.28 0.38 170 -0.34 -0.66 -0.41 0.2 -0.1 0.0 -15.51 1.16 1.24 0.89 0.89 171 -0.28 -0.42 -0.84 0.2 -0.1 0.0 -20.21 1.15 1.23 0.83 0.83 172 -0.25 0.31 0.13 0.1 0.0 0.0 -17.98 0.54 0.56 0.37 0.39 173 -0.03 -1.73 -0.37 0.2 -0.3 0.0 -13.98 1.90 2.14 1.37 1.41 174 0.18 -1.41 0.40 0.2 -0.2 0.0 -12.11 1.58 1.75 1.17 1.19 175 0.33 -0.20 0.51 0.1 -0.2 0.0 -16.39 0.68 0.86 0.51 0.65 176 0.24 -1.18 -0.03 0.2 -0.2 0.0 -13.67 1.50 1.64 1.16 1.16 177 0.30 -0.94 -0.47 0.2 -0.2 0.0 -17.79 1.36 1.52 1.04 1.06 178 0.52 -0.62 0.31 0.2 -0.1 0.0 -15.65 1.07 1.17 0.85 0.86 179 0.61 0.35 0.85 0.1 -0.1 0.0 -17.57 0.92 0.97 0.58 0.61 180 0.58 -0.39 -0.13 0.2 -0.1 0.0 -18.72 1.09 1.17 0.89 0.89 181 0.67 0.59 0.41 0.1 0.0 0.0 -21.13 0.89 0.92 0.57 0.58 182 0.89 -1.46 -0.10 0.2 -0.3 0.0 -16.30 1.85 2.09 1.37 1.42 183 1.10 -1.14 0.68 0.2 -0.2 0.0 -12.45 1.72 1.89 1.26 1.28 184 1.04 -0.25 0.01 0.1 -0.3 0.0 -21.13 1.08 1.32 0.78 0.93 185 1.25 0.07 0.78 0.1 -0.2 0.0 -19.04 1.25 1.39 0.82 0.91 186 1.16 -0.90 0.24 0.2 -0.2 0.0 -16.17 1.64 1.78 1.25 1.26 187 1.22 -0.67 -0.19 0.2 -0.2 0.0 -19.62 1.52 1.67 1.14 1.16 188 1.44 -0.35 0.58 0.2 -0.1 0.0 -16.92 1.50 1.60 1.07 1.08 189 1.50 -0.11 0.15 0.2 -0.1 0.0 -20.57 1.52 1.60 1.11 1.10 190 1.87 -0.95 -0.26 0.3 -0.2 0.0 -19.16 2.15 2.33 1.57 1.59 191 2.15 -0.39 0.08 0.2 -0.2 0.0 -19.70 2.01 2.16 1.41 1.42 192 2.42 0.16 0.42 0.2 -0.1 0.0 -19.67 2.16 2.26 1.46 1.44 193 3.13 0.12 -0.08 0.2 -0.2 0.0 -21.53 2.73 2.86 1.83 1.81 194 3.40 0.67 0.26 0.2 0.0 0.0 -21.85 2.95 3.08 1.93 1.90 195 3.46 0.91 -0.17 0.2 0.0 0.0 -23.67 3.08 3.22 2.03 2.01 196 -2.55 0.87 1.83 0.0 0.0 0.0 -10.83 2.61 2.71 1.54 1.56 197 -2.49 1.11 1.40 0.0 0.0 0.0 -12.83 2.45 2.55 1.42 1.43 198 -2.43 1.34 0.96 0.0 0.0 0.0 -14.90 2.35 2.45 1.39 1.41 199 -2.43 1.34 0.96 0.0 0.1 0.0 -15.50 2.36 2.47 1.35 1.34 200 -1.66 0.41 1.13 0.0 -0.1 0.0 -13.65 1.65 1.73 0.97 1.05 201 -1.79 1.06 0.90 0.0 -0.1 0.0 -13.73 1.81 1.91 1.10 1.20 202 -1.63 1.14 2.11 0.0 0.0 0.0 -11.20 2.32 2.42 1.35 1.40 203 -1.57 1.38 1.67 0.0 0.0 0.0 -14.45 2.14 2.23 1.22 1.25 204 -1.51 1.62 1.24 0.0 0.0 0.0 -15.23 2.03 2.11 1.19 1.23 205 -1.38 -1.41 0.19 0.3 -0.2 0.0 -12.43 2.10 2.28 1.48 1.52 206 -1.11 -0.85 0.53 0.2 -0.2 0.0 -12.85 1.59 1.74 1.13 1.19 207 -0.74 0.68 1.41 0.0 -0.1 0.0 -15.77 1.39 1.46 0.81 0.92 208 -1.05 -0.61 0.09 0.2 -0.2 0.0 -13.93 1.51 1.62 1.10 1.14 209 -0.46 -1.13 0.47 0.3 -0.2 0.0 -12.63 1.71 1.90 1.32 1.38 210 -0.19 -0.58 0.81 0.2 -0.2 0.0 -13.98 1.31 1.46 1.02 1.10 211 -0.13 -0.34 0.37 0.2 -0.2 0.0 -16.32 1.21 1.32 1.00 1.04 212 0.46 -0.86 0.74 0.3 -0.2 0.0 -14.98 1.66 1.85 1.32 1.39 213 0.52 -0.62 0.31 0.2 -0.3 0.0 -17.23 1.41 1.64 1.16 1.27 214 0.73 -0.30 1.08 0.2 -0.2 0.0 -14.46 1.47 1.62 1.12 1.19 215 0.79 -0.07 0.65 0.2 -0.2 0.0 -17.96 1.39 1.50 1.10 1.15 216 0.85 0.17 0.21 0.2 -0.2 0.0 -20.72 1.24 1.36 0.99 1.06 217 1.22 -0.67 -0.19 0.3 -0.3 0.0 -20.98 1.99 2.19 1.60 1.65 218 1.50 -0.11 0.15 0.3 -0.2 0.0 -21.25 1.79 1.94 1.39 1.44 ----End of helix scanning---- Accepted moves after helix length constraints: 9361 Accepted moves after all screens: 218 Time for screens: 47.45 Time for contact E: 0.04 ------------------------------------------------ Accepted moves after contact E screen: 30 ================================================== Selected moves based on contact/charge potential: ================================================== 1 201 1.81 2 197 2.45 3 198 2.35 4 194 2.95 5 93 1.40 6 9 1.94 7 142 3.12 8 135 1.63 9 203 2.14 10 196 2.61 11 216 1.24 12 192 2.16 13 218 1.79 14 29 1.48 15 2 1.47 16 146 3.22 17 19 1.28 18 4 1.64 19 15 1.55 20 193 2.73 21 151 1.23 22 1 1.33 23 143 3.11 24 204 2.03 25 30 1.11 26 47 1.51 27 148 2.20 28 3 1.52 29 202 2.32 30 5 1.38 31 144 3.28 32 43 2.43 33 195 3.08 34 130 1.17 35 42 2.33 36 137 2.19 37 13 2.92 38 118 0.63 39 35 1.74 40 147 3.29 41 184 1.08 42 181 0.89 43 217 1.99 44 81 1.21 45 91 3.61 46 189 1.52 47 171 1.15 48 41 2.71 49 79 1.25 50 117 0.64 51 191 2.01 ================================================ # of moves after low-resolution filtering: 51 ================================================ Minimizing initial helix ... STARTING TO WORK ON MINIMIZATION: Dynamic memory allocation: 0.000000000000000 number of degrees of freedom: 930 number of sparse matrix elements: 16593 memory allocated for hessian ME: 20150 itn. f |g| #cg mode |r| lambda nfg time 0 -2877.573 13.18263 1 -2915.685 11.36766 1 0 86.77888 1.00000 2 0.20 0.097 2 -2987.895 2.20166 3 0 33.50356 1.00000 3 0.37 0.097 3 -2992.195 2.94895 7 2 426.47043 0.02267 7 0.94 0.104 4 -2997.645 2.73573 10 2 79.49385 0.14397 10 1.48 0.133 5 -3004.336 3.01001 11 0 4.04413 0.36814 12 2.12 0.150 6 -3013.665 2.01938 10 0 2.68874 1.00000 13 2.57 0.191 7 -3014.324 2.06087 7 2 220.95072 0.01159 20 3.24 0.190 8 -3018.226 3.49813 8 0 1.85537 1.00000 21 3.62 0.194 9 -3024.096 0.96074 5 0 2.74317 1.00000 22 3.98 0.198 10 -3024.360 2.23095 19 0 0.73039 1.00000 23 4.80 0.208 11 -3026.345 0.21160 4 0 1.36712 1.00000 24 5.12 0.212 12 -3026.494 0.89543 20 3 0.35352 1.00000 25 5.99 0.217 13 -3026.875 0.03616 4 0 0.41759 1.00000 26 6.31 0.217 14 -3026.910 0.27272 30 3 0.06660 1.00000 27 7.59 0.219 15 -3026.953 0.00470 3 0 0.13366 1.00000 28 7.87 0.219 final -3026.95270 0.00470 142 0 0.13366 1.00000 28 7.87 Total time elapsed 7.870 Preliminaries 0.110 PCG Hd products 5.640 Long Range Forces 0.720 Preconditioning 0.310 Line searches 1.070 MINIMIZATION COMPLETED COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 75.288111 100.372961 140.460357 316.121429 SGB 6311.663801 -2781.917218 -2386.154074 1143.592509 TOTAL 6386.951911 -2681.544257 -2245.693716 1459.713938 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 330.433813 -396.435922 -12.710446 -78.712555 EL 2047.152907 -4535.816651 90.449388 -2398.214356 SGB -2386.154074 3002.007207 -103.633883 512.219250 TOTAL -8.567354 -1930.245366 -25.894941 -1964.707661 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4945.271317 NONPOLAR 25.330137 SGB TOT -903.305484 SOLV TOT -877.975347 TOTALE -3038.780830 STARTING TO WORK ON MINIMIZATION: Dynamic memory allocation: 0.000000000000000 number of degrees of freedom: 930 number of sparse matrix elements: 16593 memory allocated for hessian ME: 20150 itn. f |g| #cg mode |r| lambda nfg time 0 -3038.781 0.17429 1 -3038.923 0.15252 5 0 1.04858 1.00000 2 0.36 0.008 2 -3038.934 0.01863 2 0 0.57384 1.00000 3 0.50 0.008 3 -3038.950 0.04872 30 3 0.06921 1.00000 4 1.77 0.018 4 -3038.951 0.00136 2 0 0.04145 1.00000 5 1.91 0.018 5 -3038.951 0.00013 40 3 0.00212 1.00000 6 3.59 0.018 final -3038.95116 0.00013 79 3 0.00212 1.00000 6 3.59 Total time elapsed 3.590 Preliminaries 0.110 PCG Hd products 3.120 Long Range Forces 0.000 Preconditioning 0.150 Line searches 0.200 MINIMIZATION COMPLETED COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 75.344550 100.147727 140.505611 315.997888 SGB 6311.105303 -2782.087073 -2385.836064 1143.182166 TOTAL 6386.449852 -2681.939346 -2245.330453 1459.180054 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 330.543679 -395.564400 -12.705362 -77.726083 EL 2047.436295 -4536.483417 90.556593 -2398.490528 SGB -2385.836064 3001.957668 -103.678440 512.443163 TOTAL -7.856090 -1930.090149 -25.827210 -1963.773448 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4944.737565 NONPOLAR 26.404464 SGB TOT -903.276172 SOLV TOT -876.871708 TOTALE -3037.090431 WARNING: Serious failure in tn minimization dE = 1.690398396839555 Will revert to starting coordinates ... Summary for structure: MINIMIZED HELIX: ENERGY -3038.781 Global, backbone 0.230 Global, all heavy at 0.381 Local, N/CA/C/O 0.242 Local, all heavy ato 0.373 Summary of side chain addition/minim: Initial 0.00 0.00 0.00 0.00 WARNING: Serious failure in tn minimization dE = 3.085922916360687 Will revert to starting coordinates ... Pass 1 -2877.56 -3040.35 -162.78 34.00 0.24 0.75 0.26 0.75 WARNING: sampling failure in side opt: 3.017581503559995 (will revert to previous best ...) Pass 2 -3040.34 -3040.34 0.00 31.13 0.24 0.75 0.26 0.75 Summary for structure: SIDE OPT HELIX: ENERGY -3040.344 Global, backbone 0.245 Global, all heavy at 0.753 Local, N/CA/C/O 0.257 Local, all heavy ato 0.746 ------------------------------------------------- Now start clustering the helices ... ------------------------------------------------- Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 7 34 0.63 1.63 1.17 1.44 2 15 16 2.16 3.61 3.22 2.17 3 11 28 1.11 1.94 1.52 1.54 4 7 11 1.08 2.01 1.24 1.74 5 11 27 1.23 2.61 2.20 1.75 Data selected from clustering: 5 1.17 3.22 Big cluster found: 5 1.748671278333758 Clusters added; will try again ... Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 10 44 0.63 2.92 1.21 2.11 2 12 16 2.16 3.61 3.22 1.82 3 10 28 1.11 1.94 1.52 1.37 4 7 11 1.08 2.01 1.24 1.74 5 2 1 1.23 1.81 1.81 0.71 6 3 26 1.40 1.55 1.51 1.49 7 7 2 2.03 2.61 2.45 1.05 Data selected from clustering: 7 1.21 3.22 WARNING: cluster_drive ntry maxed out =================== Working on cluster (HELIX) 1 shift (z): 1.50 trans (x): -0.11 trans (y): 0.15 yaw: 0.02 pitch: -0.04 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 -156.31 -150.50 WARNING: above phi/psi not represented by library GENback Actual angles -154.52 -156.31 Closest rotamer -150.00 -165.00 Delta 4.52 -8.69 _:ALA_28 -131.66 -32.87 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles -131.66 -32.87 Closest rotamer -125.00 -35.00 Delta 6.66 -2.13 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 2 0.68 0.74 2 0.68 0.74 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 2 0.68 0.74 2 0.68 0.74 Number of closed loops found: 2 0.50 0.08 Results of loop screening 25.00 0.01 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 2 0.56 0.58 0.61 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.5557119895487324 failed cbeta test: _:PHE_57:HZ 1.805913161878036 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 2 0.67 0.71 2 0.67 0.71 Number of closed loops found: 2 0.50 0.09 Results of loop screening 25.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 2 0.54 0.56 0.59 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.5366630254398431 failed cbeta test: _:PHE_57:HZ 1.866989138158721 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 1 0.87 0.87 1 0.87 0.87 Number of closed loops found: 1 0.50 0.09 Results of loop screening 25.00 0.00 Loops NOT rejected 1 0.68 0.68 0.68 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 1 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 89.475521 97.763781 152.769745 340.009046 SGB 6405.441826 -2804.088738 -2433.947016 1167.406072 TOTAL 6494.917347 -2706.324957 -2281.177272 1507.415118 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 338.429366 4146.888146 -12.860411 4472.457101 EL 2049.570941 -4501.787076 100.152668 -2352.063467 SGB -2433.947016 3043.086609 -113.187065 495.952528 TOTAL -45.946709 2688.187679 -25.894808 2616.346162 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5020.520238 NONPOLAR 21.118797 SGB TOT -923.214622 SOLV TOT -902.095824 TOTALE 1558.306855 Summary for structure: INITIAL ENERGY 1558.307 Global, backbone 0.679 Global, all heavy at 1.294 Local, N/CA/C/O 0.718 Local, all heavy ato 1.180 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -42.12 178.73 _:ASN_42 -88.70 9.85 173.51 _:GLY_43 75.63 21.99 -179.46 _:VAL_44 -92.43 126.32 179.56 _:ASP_45 -130.87 95.99 -174.44 _:GLY_46 -139.43 -167.87 179.52 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.65 2.65 1 2.65 2.65 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.37 15 2.03 6.10 15 2.03 6.10 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.65 2.65 1 2.65 2.65 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.38 15 2.03 6.10 15 2.03 6.10 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.36 2.36 1 2.36 2.36 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.41 16 2.01 6.10 16 2.01 6.10 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.44 2.44 1 2.44 2.44 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.65 23 1.72 6.20 23 1.72 6.20 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.67 2.67 1 2.67 2.67 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.80 33 1.72 6.34 33 1.72 6.34 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 13 0.85 3.02 13 0.85 3.02 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.08 52 0.91 6.21 52 0.91 6.21 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 13 0.83 2.86 13 0.83 2.86 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.41 54 1.43 6.10 54 1.43 6.10 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 9 0.96 3.52 9 0.96 3.52 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.63 96 1.18 6.10 96 1.18 6.10 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 22 0.89 3.98 22 0.89 3.98 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 2.85 134 1.60 6.34 134 1.60 6.34 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 36 0.63 3.98 36 0.63 3.98 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 6.02 411 1.18 6.17 411 1.18 6.17 Number of closed loops found: 7 0.40 0.10 Results of loop screening 25.00 0.01 Loops NOT rejected 2 1.14 1.32 1.49 Loops rejected for theta 1 1.17 1.17 1.17 Loops rejected for phi/psi 4 1.29 1.48 1.99 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 1.0 2.0 2 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 94.551638 102.329703 169.330509 366.211851 SGB 6403.806987 -2804.292174 -2436.923783 1162.591030 TOTAL 6498.358625 -2701.962471 -2267.593274 1528.802880 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 354.790783 72.028455 -12.697416 414.121822 EL 2061.654685 -4538.843172 114.377369 -2362.811118 SGB -2436.923783 3078.743341 -126.270073 515.549485 TOTAL -20.478316 -1388.071375 -24.590120 -1433.139811 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5015.731164 NONPOLAR 23.797788 SGB TOT -900.666866 SOLV TOT -876.869078 TOTALE -2459.346523 Summary for structure: INITIAL ENERGY -2459.347 Global, backbone 1.142 Global, all heavy at 2.546 Local, N/CA/C/O 0.933 Local, all heavy ato 2.071 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -105.00 -55.00 -180.00 _:ASP_27 -95.00 100.00 176.68 _:ALA_28 -31.47 -20.51 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles -31.47 -20.51 Closest rotamer -45.00 -30.00 Delta -13.53 -9.49 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 1.04 1.04 1 1.04 1.04 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 1.04 1.04 1 1.04 1.04 Number of closed loops found: 1 0.50 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 1 0.78 0.78 0.78 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 1 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 95.264987 102.664270 169.627202 367.556460 SGB 6460.906593 -2827.149084 -2439.350726 1194.406783 TOTAL 6556.171580 -2724.484814 -2269.723524 1561.963243 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 354.792118 33.201157 -12.698615 375.294660 EL 2061.769456 -4493.674713 135.271991 -2296.633266 SGB -2439.350726 3069.585038 -146.611344 483.622968 TOTAL -22.789152 -1390.888518 -24.037968 -1437.715637 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5049.420886 NONPOLAR 27.626331 SGB TOT -932.040409 SOLV TOT -904.414078 TOTALE -2458.196224 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 95.264987 102.664270 169.627202 367.556460 SGB 6460.906593 -2827.149084 -2439.350726 1194.406783 TOTAL 6556.171580 -2724.484814 -2269.723524 1561.963243 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 354.792118 33.201157 -12.698615 375.294660 EL 2061.769456 -4493.674713 135.271991 -2296.633266 SGB -2439.350726 3069.585038 -146.611344 483.622968 TOTAL -22.789152 -1390.888518 -24.037968 -1437.715637 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5049.420886 NONPOLAR 27.626331 SGB TOT -932.040409 SOLV TOT -904.414078 TOTALE -2458.196224 Summary for structure: INITIAL ENERGY -2458.196 Global, backbone 0.679 Global, all heavy at 1.294 Local, N/CA/C/O 0.718 Local, all heavy ato 1.180 Parameters for generating loops ... Minimum conformations: 16 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 1 1.04 1.04 1 1.04 1.04 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 1.04 1.04 1 1.04 1.04 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 2 1.07 1.18 2 1.07 1.18 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 0.72 0.72 1 0.72 0.72 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 2 0.72 1.04 2 0.72 1.04 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.13 4 0.76 1.18 4 0.76 1.18 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.21 21 0.54 1.16 21 0.54 1.16 Number of closed loops found: 21 0.20 0.09 Results of loop screening 20.00 0.03 Loops NOT rejected 13 0.43 0.49 0.78 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 1 0.81 0.81 0.81 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 7 0.46 0.52 0.60 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 13 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.34 672 0.42 1.22 672 0.42 1.22 Number of closed loops found: 672 0.10 0.12 Results of loop screening 20.00 0.88 Loops NOT rejected 355 0.37 0.52 0.78 Loops rejected for theta 191 0.42 0.60 0.80 Loops rejected for phi/psi 44 0.49 0.64 0.84 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 82 0.40 0.50 0.60 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 355 CLUSTERING PARAMETERS Number of data points: 355 Number of descriptors: 36 Number of clusters: 8 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.010 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 29 121 0.37 0.55 0.41 0.66 2 57 236 0.42 0.64 0.50 0.76 3 56 269 0.41 0.60 0.45 0.60 4 38 294 0.46 0.61 0.56 0.59 5 21 227 0.41 0.49 0.43 0.49 6 44 44 0.38 0.54 0.48 0.65 7 56 190 0.55 0.78 0.59 0.64 8 54 11 0.40 0.68 0.44 0.73 Data selected from clustering: 8 0.41 0.59 Big cluster found: 8 0.7310651148108109 Clusters added; will try again ... Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 28 121 0.37 0.55 0.41 0.64 2 57 236 0.42 0.64 0.50 0.76 3 56 269 0.41 0.60 0.45 0.60 4 38 294 0.46 0.61 0.56 0.59 5 21 227 0.41 0.49 0.43 0.49 6 41 131 0.38 0.54 0.47 0.61 7 56 190 0.55 0.78 0.59 0.64 8 26 39 0.40 0.53 0.41 0.55 9 18 2 0.43 0.61 0.50 0.55 10 14 59 0.55 0.68 0.58 0.51 Data selected from clustering: 10 0.41 0.59 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.41 1.46 0.31 1.27 Pass 1 -822.26 -2645.16 -1822.91 3.19 0.43 1.05 0.27 1.04 Pass 2 -2645.16 -2645.33 -0.16 3.62 0.43 0.86 0.27 0.86 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 0.50 1.41 0.49 1.24 Pass 1 -2310.03 -2646.95 -336.92 2.37 0.49 1.37 0.39 1.15 Pass 2 -2646.95 -2646.88 0.07 3.01 0.49 1.38 0.38 1.16 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 0.45 1.26 0.27 1.16 Pass 1 -1018.83 -2647.78 -1628.95 2.84 0.44 0.85 0.27 0.85 Pass 2 -2647.78 -2647.70 0.08 3.01 0.43 0.87 0.27 0.86 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 0.56 1.29 0.47 1.23 Pass 1 -2510.15 -2646.39 -136.24 2.23 0.48 1.17 0.30 1.08 Pass 2 -2646.39 -2646.79 -0.39 3.76 0.46 1.21 0.28 1.11 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 0.43 1.33 0.30 1.16 Pass 1 -1164.51 -2643.60 -1479.09 3.32 0.47 1.20 0.29 1.09 Pass 2 -2643.60 -2643.34 0.26 3.15 0.46 1.23 0.28 1.11 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.47 1.36 0.45 1.24 Pass 1 -2504.12 -2644.99 -140.87 1.92 0.47 1.20 0.29 1.09 Pass 2 -2644.99 -2644.99 0.00 3.11 0.46 1.22 0.28 1.11 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.59 1.27 0.55 1.20 Pass 1 -2548.16 -2651.45 -103.28 2.18 0.50 1.33 0.44 1.15 Pass 2 -2651.45 -2651.65 -0.20 2.80 0.50 1.33 0.44 1.16 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 0.41 1.42 0.21 1.28 Pass 1 -2207.87 -2646.18 -438.30 2.57 0.43 1.05 0.27 1.05 Pass 2 -2646.18 -2646.05 0.12 2.95 0.43 0.87 0.27 0.86 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 0.50 1.59 0.21 1.29 WARNING: exceeded maximum steps in line search WARNING: Serious failure in tn minimization dE = 3.235599155271757 Will revert to starting coordinates ... Pass 1 -1768.69 -2645.64 -876.95 3.17 0.47 1.30 0.25 1.17 WARNING: sampling failure in side opt: 2.886532613179497 (will revert to previous best ...) Pass 2 -2645.63 -2645.63 0.00 4.55 0.47 1.30 0.25 1.17 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 0.58 1.45 0.26 1.20 Pass 1 -2351.76 -2641.15 -289.39 2.39 0.43 0.85 0.27 0.85 Pass 2 -2641.15 -2640.85 0.30 2.97 0.43 0.86 0.27 0.86 Results so far: 7 190 -2651.65 0.50 1.33 0.44 1.16 3 269 -2647.70 0.43 0.87 0.27 0.86 2 236 -2646.88 0.49 1.38 0.38 1.16 4 294 -2646.79 0.46 1.21 0.28 1.11 8 39 -2646.05 0.43 0.87 0.27 0.86 9 2 -2645.63 0.47 1.30 0.25 1.17 1 121 -2645.33 0.43 0.86 0.27 0.86 6 131 -2644.99 0.46 1.22 0.28 1.11 5 227 -2643.34 0.46 1.23 0.28 1.11 10 59 -2640.85 0.43 0.86 0.27 0.86 Initial Minimized Side Opt Final ENERGY -2458.196 0.000 0.000 -2651.652 Global, ba 0.679 0.000 0.000 0.503 Global, al 1.294 0.000 0.000 1.333 Local, N/C 0.718 0.000 0.000 0.442 Local, all 1.180 0.000 0.000 1.156 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_27:OD1 [No apparent H-bonds] _:ASP_27:OD2 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -42.12 178.73 _:ASN_42 70.00 5.00 174.22 _:GLY_43 -139.70 177.69 -180.00 _:VAL_44 -130.00 -180.00 -180.00 _:ASP_45 -10.00 -75.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -10.00 -75.00 Closest rotamer -45.00 -55.00 Delta -35.00 20.00 _:GLY_46 160.00 -165.00 179.52 Gamma turn in _:ASN_42 70.00 5.00 174.22 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.65 2.65 1 2.65 2.65 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.38 15 2.03 6.10 15 2.03 6.10 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.65 2.65 1 2.65 2.65 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.38 15 2.03 6.10 15 2.03 6.10 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.36 2.36 1 2.36 2.36 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.41 16 2.01 6.10 16 2.01 6.10 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.44 2.44 1 2.44 2.44 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.66 23 1.72 6.20 23 1.72 6.20 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.67 2.67 1 2.67 2.67 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.81 33 1.72 6.34 33 1.72 6.34 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 13 0.85 3.02 13 0.85 3.02 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.09 52 0.91 6.21 52 0.91 6.21 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 13 0.83 2.86 13 0.83 2.86 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.41 54 1.43 6.10 54 1.43 6.10 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 9 0.96 3.52 9 0.96 3.52 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.64 96 1.18 6.10 96 1.18 6.10 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 22 0.89 3.98 22 0.89 3.98 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 2.87 134 1.60 6.34 134 1.60 6.34 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 36 0.63 3.98 36 0.63 3.98 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 6.04 411 1.18 6.17 411 1.18 6.17 Number of closed loops found: 7 0.40 0.11 Results of loop screening 20.00 0.01 Loops NOT rejected 2 1.14 1.32 1.49 Loops rejected for theta 2 1.17 1.58 1.99 Loops rejected for phi/psi 3 1.29 1.30 1.31 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 1.0 2.0 2 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 112134.334677 690.805807 169.845624 112994.986108 SGB 6506.008412 -2849.973609 -2412.566074 1243.468729 TOTAL 118640.343089 -2159.167803 -2242.720450 114238.454836 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 367.392972 2022.151627 -12.260127 2377.284472 EL 2030.441205 -4535.399792 144.714359 -2360.244228 SGB -2412.566074 3099.131658 -155.736594 530.828990 TOTAL -14.731897 585.883493 -23.282362 547.869234 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5094.060839 NONPOLAR 15.112076 SGB TOT -907.197046 SOLV TOT -892.084970 TOTALE 112119.941381 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 112134.334677 690.805807 169.845624 112994.986108 SGB 6506.008412 -2849.973609 -2412.566074 1243.468729 TOTAL 118640.343089 -2159.167803 -2242.720450 114238.454836 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 367.392972 2022.151627 -12.260127 2377.284472 EL 2030.441205 -4535.399792 144.714359 -2360.244228 SGB -2412.566074 3099.131658 -155.736594 530.828990 TOTAL -14.731897 585.883493 -23.282362 547.869234 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5094.060839 NONPOLAR 15.112076 SGB TOT -907.197046 SOLV TOT -892.084970 TOTALE 112119.941381 Summary for structure: INITIAL ENERGY 112119.941 Global, backbone 3.959 Global, all heavy at 4.400 Local, N/CA/C/O 3.383 Local, all heavy ato 3.822 Parameters for generating loops ... Minimum conformations: 64 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 36 0.63 3.98 36 0.63 3.98 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 6.04 411 1.18 6.17 411 1.18 6.17 Number of closed loops found: 7 0.40 0.11 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.10 92 0.50 3.50 92 0.50 3.50 Right branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 12.18 1363 0.93 6.33 1363 0.93 6.33 Number of closed loops found: 45 0.30 0.14 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.20 334 0.64 3.98 334 0.64 3.98 Right branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 44.02 6641 0.86 6.36 6641 0.86 6.36 Number of closed loops found: 590 0.20 0.36 Results of loop screening 20.00 0.94 Loops NOT rejected 242 0.67 1.34 1.85 Loops rejected for theta 206 0.70 1.42 2.25 Loops rejected for phi/psi 129 0.63 1.25 2.08 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 2 1.19 1.27 1.35 Loops rejected for sidechn 11 1.08 1.37 1.55 Histogram of accepted loops: 0.0 1.0 13 1.0 2.0 229 Best loop that was rejected: 0.6275993995855949 failed phi/psi test: 24.28022662936060 91.30573832709653 failed side test: _:VAL_44 0.5999999999999998 CLUSTERING PARAMETERS Number of data points: 242 Number of descriptors: 60 Number of clusters: 12 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.010 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 21 77 1.33 1.55 1.33 1.72 2 30 49 1.09 1.44 1.23 1.78 3 18 231 1.01 1.32 1.19 2.98 4 22 55 1.12 1.36 1.15 1.34 5 11 37 1.53 1.82 1.77 1.70 6 30 103 1.08 1.35 1.22 2.10 7 5 26 1.52 1.70 1.56 1.31 8 33 127 1.48 1.85 1.51 1.71 9 18 217 1.29 1.66 1.57 1.70 10 17 195 1.14 1.50 1.28 1.95 11 13 34 1.60 1.77 1.72 1.65 12 24 206 0.67 1.46 0.96 3.19 Data selected from clustering: 12 0.96 1.77 Big cluster found: 12 3.185835121723032 Clusters added; will try again ... Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 23 77 1.33 1.55 1.33 1.92 2 30 49 1.09 1.44 1.23 1.78 3 22 170 1.08 1.32 1.16 2.38 4 22 55 1.12 1.36 1.15 1.34 5 11 37 1.53 1.82 1.77 1.70 6 22 98 1.20 1.35 1.21 1.36 7 5 26 1.52 1.70 1.56 1.31 8 33 127 1.48 1.85 1.51 1.71 9 12 217 1.33 1.66 1.57 1.31 10 21 193 1.14 1.39 1.20 1.86 11 13 34 1.60 1.77 1.72 1.65 12 12 204 0.67 1.34 0.96 1.97 13 7 92 1.42 1.46 1.44 0.52 14 9 220 0.80 1.13 0.82 1.63 Data selected from clustering: 14 0.82 1.77 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 1.33 2.93 1.32 2.74 Pass 1 -2709.20 -2836.91 -127.71 4.05 1.36 2.95 1.08 2.39 Pass 2 -2836.91 -2836.60 0.31 3.19 1.37 2.95 1.08 2.39 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 1.23 2.88 1.25 2.85 Pass 1 -2683.82 -2825.32 -141.50 3.76 1.29 2.69 1.19 2.71 Pass 2 -2825.32 -2826.53 -1.21 3.98 1.32 2.67 1.19 2.70 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 1.16 2.86 1.18 2.57 Pass 1 -2705.44 -2825.60 -120.16 3.62 1.27 2.73 1.16 2.74 WARNING: sampling failure in side opt: 0.6893618788826643 (will revert to previous best ...) Pass 2 -2825.60 -2825.60 0.00 4.00 1.27 2.73 1.16 2.74 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 1.15 3.07 1.20 2.95 WARNING: Serious failure in tn minimization dE = 2.302457950286680 Will revert to starting coordinates ... Pass 1 -2632.39 -2828.13 -195.74 6.09 1.24 2.64 1.03 2.22 WARNING: Serious failure in tn minimization dE = 2.329060912747536 Will revert to starting coordinates ... WARNING: Minimization may not be converged. Pass 2 -2828.13 -2830.25 -2.12 6.12 1.25 2.65 1.03 2.22 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 1.77 3.04 1.48 3.00 Pass 1 -2632.03 -2806.45 -174.42 2.76 1.74 2.85 1.36 2.79 Pass 2 -2806.45 -2808.17 -1.72 3.31 1.74 2.85 1.36 2.79 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 1.21 3.08 1.21 2.75 WARNING: Serious failure in tn minimization dE = 2.365093470413740 Will revert to starting coordinates ... Pass 1 -2664.98 -2829.66 -164.67 4.90 1.24 2.64 1.03 2.21 WARNING: sampling failure in side opt: 4.049598898406202 (will revert to previous best ...) Pass 2 -2829.66 -2829.66 0.00 5.54 1.24 2.64 1.03 2.21 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 1.56 3.05 1.38 2.78 Pass 1 -2631.57 -2824.97 -193.40 5.33 1.52 3.33 1.34 2.66 Pass 2 -2824.97 -2824.69 0.28 4.11 1.52 3.32 1.34 2.66 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 1.51 3.45 1.35 2.96 Pass 1 -2656.27 -2821.16 -164.89 2.94 1.38 3.15 1.31 2.73 Pass 2 -2821.16 -2821.36 -0.20 4.07 1.38 3.16 1.31 2.73 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 1.57 3.46 1.27 2.84 Pass 1 -2620.85 -2826.14 -205.29 3.02 1.35 2.74 1.08 2.25 Pass 2 -2826.14 -2826.55 -0.41 5.56 1.25 2.52 0.97 2.05 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 1.20 3.16 1.12 2.69 Pass 1 -2661.70 -2823.10 -161.40 4.73 1.24 2.72 1.00 2.21 Pass 2 -2823.10 -2823.01 0.09 4.19 1.24 2.72 1.00 2.21 =================== Working on cluster 11 Summary of side chain addition/minim: Initial 1.72 2.89 1.36 2.78 Pass 1 -2697.13 -2827.47 -130.34 3.33 1.30 2.73 1.21 2.62 Pass 2 -2827.47 -2828.99 -1.52 4.88 1.30 2.69 1.21 2.59 =================== Working on cluster 12 Summary of side chain addition/minim: Initial 0.96 2.39 0.82 1.93 WARNING: Serious failure in tn minimization dE = 2.685321329700400 Will revert to starting coordinates ... Pass 1 -2682.21 -2839.56 -157.35 4.57 1.00 2.39 0.90 2.02 WARNING: Serious failure in tn minimization dE = 1.092865813063781 Will revert to starting coordinates ... WARNING: Minimization may not be converged. WARNING: sampling failure in side opt: 4.157698444093512 (will revert to previous best ...) Pass 2 -2839.56 -2839.56 0.00 6.48 1.00 2.39 0.90 2.02 =================== Working on cluster 13 Summary of side chain addition/minim: Initial 1.44 2.62 1.12 2.27 WARNING: Serious failure in tn minimization dE = 2.841709915857791 Will revert to starting coordinates ... Pass 1 -2638.26 -2817.33 -179.07 4.69 1.06 2.28 0.97 1.90 WARNING: Serious failure in tn minimization dE = 3.305001473501761 Will revert to starting coordinates ... WARNING: Minimization may not be converged. WARNING: sampling failure in side opt: 0.9895390055285134 (will revert to previous best ...) Pass 2 -2817.33 -2817.33 0.00 6.06 1.06 2.28 0.97 1.90 =================== Working on cluster 14 Summary of side chain addition/minim: Initial 0.82 1.96 0.55 1.63 Pass 1 -2624.39 -2833.60 -209.21 2.87 0.94 1.94 0.69 1.61 Pass 2 -2833.60 -2833.88 -0.28 3.44 0.94 1.94 0.69 1.61 Results so far: 12 204 -2839.56 1.00 2.39 0.90 2.02 1 77 -2836.60 1.37 2.95 1.08 2.39 14 220 -2833.88 0.94 1.94 0.69 1.61 4 55 -2830.25 1.25 2.65 1.03 2.22 6 98 -2829.66 1.24 2.64 1.03 2.21 11 34 -2828.99 1.30 2.69 1.21 2.59 9 217 -2826.55 1.25 2.52 0.97 2.05 2 49 -2826.53 1.32 2.67 1.19 2.70 3 170 -2825.60 1.27 2.73 1.16 2.74 7 26 -2824.69 1.52 3.32 1.34 2.66 10 193 -2823.01 1.24 2.72 1.00 2.21 8 127 -2821.36 1.38 3.16 1.31 2.73 13 92 -2817.33 1.06 2.28 0.97 1.90 5 37 -2808.17 1.74 2.85 1.36 2.79 Initial Minimized Side Opt Final ENERGY 112119.941 0.000 0.000 -2839.559 Global, ba 3.959 0.000 0.000 1.000 Global, al 4.400 0.000 0.000 2.388 Local, N/C 3.383 0.000 0.000 0.898 Local, all 3.822 0.000 0.000 2.021 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_41:OD1 [No apparent H-bonds] _:ASP_41:OD2 [No apparent H-bonds] _:ASN_42:OD1 [No apparent H-bonds] _:ASN_42:ND2 INTRA HBOND (side/side) _:ASP_45:OD1 _:TRP_48:NE1 1 2.746 INTRA HBOND (side/main) _:ASP_45:OD1 _:GLY_46:N 1 2.881 [No apparent H-bonds] _:ASP_45:OD2 Summary of side chain addition/minim: Initial 1.38 1.84 0.79 1.39 Pass 1 -2781.79 -3025.45 -243.66 28.79 0.65 1.47 0.55 1.43 Pass 2 -3025.45 -3030.44 -4.98 36.63 0.60 1.38 0.51 1.33 =================== Working on cluster (HELIX) 2 shift (z): 3.83 trans (x): 0.07 trans (y): -0.57 yaw: -0.19 pitch: 0.07 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 11.40 157.51 WARNING: above phi/psi not represented by library GENback Actual angles -154.52 11.40 Closest rotamer -140.00 20.00 Delta 14.52 8.60 _:ALA_28 111.09 -32.87 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles 111.09 -32.87 Closest rotamer 75.00 5.00 Delta -36.09 37.87 Gamma turn in _:ALA_28 111.09 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.16 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.18 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.26 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 1.99 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.44 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 3.21 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.45 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 3.23 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! WARNING: Could not close N-term loop shift (z): 3.56 trans (x): -0.48 trans (y): -0.91 yaw: -0.19 pitch: 0.20 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 18.49 163.62 WARNING: above phi/psi not represented by library GENback Actual angles -154.52 18.49 Closest rotamer -140.00 20.00 Delta 14.52 1.51 _:ALA_28 97.19 -32.87 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles 97.19 -32.87 Closest rotamer 75.00 5.00 Delta -22.19 37.87 Gamma turn in _:ALA_28 97.19 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.19 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.29 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.52 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.52 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! WARNING: Could not close N-term loop shift (z): 2.42 trans (x): 0.16 trans (y): 0.42 yaw: -0.19 pitch: 0.07 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 -116.39 -155.12 WARNING: above phi/psi not represented by library GENback Actual angles -154.52 -116.39 Closest rotamer -150.00 -165.00 Delta 4.52 -48.61 _:ALA_28 -167.13 -32.87 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles -167.13 -32.87 Closest rotamer -130.00 -40.00 Delta 37.13 -7.13 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 1 1.01 1.01 1 1.01 1.01 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 1 1.01 1.01 1 1.01 1.01 Number of closed loops found: 1 0.50 0.09 Results of loop screening 25.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 1 0.84 0.84 0.84 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.8396356713344019 failed theta test: 141.8300413965499 failed cbeta test: _:PHE_57:HZ 1.292634357646491 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 1 0.73 0.73 1 0.73 0.73 Number of closed loops found: 1 0.50 0.08 Results of loop screening 25.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 1 0.66 0.66 0.66 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.6647435411131819 failed cbeta test: _:PHE_57:HZ 1.330813686647264 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 0.73 0.73 1 0.73 0.73 Number of closed loops found: 1 0.40 0.08 Results of loop screening 25.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 1 0.66 0.66 0.66 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.6647435411131819 failed cbeta test: _:PHE_57:HZ 1.330813686647264 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 10 0.80 0.96 10 0.80 0.96 Number of closed loops found: 10 0.20 0.09 Results of loop screening 25.00 0.01 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 2 0.77 0.78 0.80 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 8 0.70 0.74 0.79 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.7008024247162643 failed cbeta test: _:PHE_57:HZ 1.195715803374253 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.28 194 0.72 1.04 194 0.72 1.04 Number of closed loops found: 194 0.10 0.10 Results of loop screening 25.00 0.18 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 20 0.75 0.81 0.86 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 174 0.60 0.70 0.87 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.5994983683622076 failed cbeta test: _:PHE_57:HZ 1.412232358010934 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.63 2472 0.70 1.07 2472 0.70 1.07 Number of closed loops found: 2472 0.10 0.19 Results of loop screening 25.00 2.36 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 228 0.74 0.81 0.88 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 2244 0.60 0.71 0.89 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.5950973080658915 failed cbeta test: _:PHE_57:HZ 1.465067611675461 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 87.464135 98.485686 158.993313 344.943135 SGB 6462.507891 -2818.975720 -2454.980879 1188.551292 TOTAL 6549.972027 -2720.490034 -2295.987566 1533.494427 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 339.016035 9328645.285220 -13.329141 9328970.972114 EL 2063.386786 -4468.740505 105.731505 -2299.622214 SGB -2454.980879 3091.459022 -118.989644 517.488499 TOTAL -52.578058 9327268.003737 -26.587280 9327188.838399 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5067.593785 NONPOLAR 15.639932 SGB TOT -906.573114 SOLV TOT -890.933182 TOTALE 9326125.359852 Summary for structure: INITIAL ENERGY ********** Global, backbone 0.595 Global, all heavy at 1.281 Local, N/CA/C/O 0.367 Local, all heavy ato 1.110 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.63 2472 0.70 1.07 2472 0.70 1.07 Number of closed loops found: 2472 0.10 0.20 Results of loop screening 25.00 2.37 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 228 0.74 0.81 0.88 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 2244 0.60 0.71 0.89 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.5950973080658915 failed cbeta test: _:PHE_57:HZ 1.465067611675461 WARNING: Could not close N-term loop shift (z): 3.77 trans (x): -0.17 trans (y): -0.14 yaw: -0.16 pitch: 0.12 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 -21.57 171.19 WARNING: above phi/psi not represented by library GENback Actual angles -154.52 -21.57 Closest rotamer -135.00 -5.00 Delta 19.52 16.57 _:ALA_28 130.60 -32.87 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles 130.60 -32.87 Closest rotamer 75.00 5.00 Delta -55.60 37.87 Gamma turn in _:ALA_28 130.60 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.11 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.33 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 2.22 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.49 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 4.61 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.15 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.74 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 6.33 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.14 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.74 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 6.36 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! WARNING: Could not close N-term loop shift (z): 3.46 trans (x): 0.91 trans (y): -0.17 yaw: -0.24 pitch: -0.02 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 177.00 -67.85 _:ALA_28 171.65 -32.87 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles 171.65 -32.87 Closest rotamer -130.00 -40.00 Delta 58.35 -7.13 Cis peptide in _:ASP_27 -154.52 177.00 -67.85 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.30 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.97 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.11 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.42 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 3.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.55 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 4.45 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.55 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 4.47 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! WARNING: Could not close N-term loop =================== Working on cluster (HELIX) 3 shift (z): 0.98 trans (x): -0.49 trans (y): 0.45 yaw: 0.23 pitch: -0.10 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 -135.56 -166.11 WARNING: above phi/psi not represented by library GENback Actual angles -154.52 -135.56 Closest rotamer -150.00 -165.00 Delta 4.52 -29.44 _:ALA_28 -135.78 -32.87 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles -135.78 -32.87 Closest rotamer -130.00 -40.00 Delta 5.78 -7.13 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 0.75 0.75 1 0.75 0.75 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 0.75 0.75 1 0.75 0.75 Number of closed loops found: 1 0.50 0.08 Results of loop screening 25.00 0.01 Loops NOT rejected 1 0.63 0.63 0.63 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 1 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 75.137121 100.338944 160.244554 335.720620 SGB 6414.212977 -2804.513481 -2438.210242 1171.489255 TOTAL 6489.350099 -2704.174536 -2277.965688 1507.209875 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 342.980445 -131.249967 -12.486897 199.243581 EL 2066.478119 -4500.519859 101.276252 -2332.765488 SGB -2438.210242 3056.056416 -115.025828 502.820346 TOTAL -28.751678 -1575.713411 -26.236473 -1630.701561 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5027.904541 NONPOLAR 19.784511 SGB TOT -915.384698 SOLV TOT -895.600187 TOTALE -2693.401475 Summary for structure: INITIAL ENERGY -2693.401 Global, backbone 0.627 Global, all heavy at 1.564 Local, N/CA/C/O 0.696 Local, all heavy ato 1.330 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -35.80 179.33 _:ASN_42 -94.96 9.85 173.51 _:GLY_43 75.63 21.99 -180.00 _:VAL_44 -180.00 115.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -180.00 115.00 Closest rotamer -165.00 105.00 Delta 15.00 -10.00 _:ASP_45 -75.00 -80.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -75.00 -80.00 Closest rotamer -80.00 -75.00 Delta -5.00 5.00 _:GLY_46 165.00 -175.00 179.52 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.60 2.60 1 2.60 2.60 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.31 19 1.49 6.07 19 1.49 6.07 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.35 21 1.49 6.07 21 1.49 6.07 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.60 2.60 1 2.60 2.60 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.34 21 1.49 6.07 21 1.49 6.07 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.32 2.32 1 2.32 2.32 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.55 31 1.49 6.08 31 1.49 6.08 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.50 2.50 1 2.50 2.50 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.70 34 1.49 5.83 34 1.49 5.83 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 13 0.58 2.82 13 0.58 2.82 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.08 59 1.49 6.09 59 1.49 6.09 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 15 0.77 3.03 15 0.77 3.03 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.28 70 1.30 5.82 70 1.30 5.82 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 11 1.47 3.29 11 1.47 3.29 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.61 115 1.44 5.84 115 1.44 5.84 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 17 1.10 3.69 17 1.10 3.69 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 2.66 167 0.70 5.85 167 0.70 5.85 Number of closed loops found: 0 0.50 0.10 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 32 0.55 3.70 32 0.55 3.70 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 5.67 530 0.70 6.07 530 0.70 6.07 Number of closed loops found: 10 0.40 0.11 Results of loop screening 25.00 0.01 Loops NOT rejected 4 0.57 1.24 2.13 Loops rejected for theta 2 0.99 1.43 1.87 Loops rejected for phi/psi 4 1.25 1.56 1.95 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 1 1.0 2.0 2 2.0 3.0 1 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 88.665394 105.850544 167.849941 362.365879 SGB 6474.204809 -2816.661025 -2480.565263 1176.978520 TOTAL 6562.870203 -2710.810482 -2312.715322 1539.344399 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 355.665734 -219.202838 13.582194 150.045090 EL 2074.696813 -4536.004688 126.795234 -2334.512641 SGB -2480.565263 3113.797626 -138.504219 494.728144 TOTAL -50.202716 -1641.409900 1.873209 -1689.739407 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5068.528098 NONPOLAR 24.337951 SGB TOT -916.256170 SOLV TOT -891.918219 TOTALE -2714.019892 Summary for structure: INITIAL ENERGY -2714.020 Global, backbone 0.570 Global, all heavy at 1.621 Local, N/CA/C/O 0.674 Local, all heavy ato 1.606 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -80.00 -75.00 -180.00 _:ASP_27 -100.00 115.00 176.13 _:ALA_28 -32.24 -17.20 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles -32.24 -17.20 Closest rotamer -45.00 -30.00 Delta -12.76 -12.80 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 1 1.41 1.41 1 1.41 1.41 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 1 1.41 1.41 1 1.41 1.41 Number of closed loops found: 1 0.50 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 1 1.03 1.03 1.03 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.026135077972351 failed phi/psi test: 73.21452940872253 -43.01156641465815 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 2 0.96 1.41 2 0.96 1.41 Number of closed loops found: 2 0.50 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 1 0.77 0.77 0.77 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 1 1.03 1.03 1.03 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 1 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 97.447491 106.685515 168.181393 372.314399 SGB 6413.816056 -2808.931183 -2434.346772 1170.538102 TOTAL 6511.263548 -2702.245668 -2266.165379 1542.852501 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 355.675257 -74.291125 -13.104052 268.280081 EL 2074.717504 -4501.434917 133.255760 -2293.461652 SGB -2434.346772 3101.441386 -145.507912 521.586702 TOTAL -3.954010 -1474.284655 -25.356204 -1503.594870 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5016.577397 NONPOLAR 20.695496 SGB TOT -890.105822 SOLV TOT -869.410326 TOTALE -2522.277499 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 97.447491 106.685515 168.181393 372.314399 SGB 6413.816056 -2808.931183 -2434.346772 1170.538102 TOTAL 6511.263548 -2702.245668 -2266.165379 1542.852501 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 355.675257 -74.291125 -13.104052 268.280081 EL 2074.717504 -4501.434917 133.255760 -2293.461652 SGB -2434.346772 3101.441386 -145.507912 521.586702 TOTAL -3.954010 -1474.284655 -25.356204 -1503.594870 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5016.577397 NONPOLAR 20.695496 SGB TOT -890.105822 SOLV TOT -869.410326 TOTALE -2522.277499 Summary for structure: INITIAL ENERGY -2522.277 Global, backbone 0.627 Global, all heavy at 1.564 Local, N/CA/C/O 0.696 Local, all heavy ato 1.330 Parameters for generating loops ... Minimum conformations: 16 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 2 0.96 1.41 2 0.96 1.41 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.10 1 1.41 1.41 1 1.41 1.41 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.11 2 0.87 1.34 2 0.87 1.34 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.15 3 0.75 1.34 3 0.75 1.34 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.29 15 0.73 1.41 15 0.73 1.41 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 2.00 620 0.40 1.41 620 0.40 1.41 Number of closed loops found: 620 0.10 0.11 Results of loop screening 20.00 0.82 Loops NOT rejected 365 0.34 0.52 0.82 Loops rejected for theta 194 0.42 0.62 1.00 Loops rejected for phi/psi 61 0.48 0.69 1.03 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 365 CLUSTERING PARAMETERS Number of data points: 365 Number of descriptors: 36 Number of clusters: 8 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 47 45 0.36 0.63 0.41 0.66 2 48 59 0.43 0.64 0.46 0.73 3 55 113 0.34 0.48 0.39 0.70 4 46 141 0.38 0.52 0.44 0.64 5 35 309 0.55 0.82 0.59 0.79 6 57 338 0.54 0.79 0.65 0.81 7 47 179 0.42 0.67 0.45 0.64 8 30 88 0.45 0.66 0.51 0.78 Data selected from clustering: 8 0.39 0.65 Big cluster found: 8 0.7827960200509306 Clusters added; will try again ... Summary of cluster results; time = 0.010 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 43 45 0.36 0.57 0.41 0.58 2 44 59 0.43 0.64 0.46 0.62 3 40 112 0.34 0.46 0.37 0.52 4 59 141 0.38 0.57 0.44 0.76 5 44 317 0.55 0.82 0.62 0.78 6 41 351 0.56 0.79 0.63 0.74 7 45 179 0.42 0.67 0.45 0.63 8 20 87 0.45 0.66 0.50 0.54 9 19 17 0.40 0.67 0.41 0.67 10 10 12 0.43 0.53 0.48 0.49 Data selected from clustering: 10 0.37 0.63 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.41 1.36 0.35 1.24 Pass 1 -2461.66 -2608.13 -146.47 2.07 0.36 0.87 0.22 0.90 Pass 2 -2608.13 -2608.02 0.11 2.94 0.35 0.87 0.21 0.90 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 0.46 0.96 0.45 0.93 Pass 1 -2559.34 -2603.17 -43.83 1.92 0.38 1.16 0.24 1.11 Pass 2 -2603.17 -2603.09 0.08 2.90 0.38 1.17 0.24 1.11 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 0.37 1.34 0.13 1.22 Pass 1 -2497.40 -2604.77 -107.37 2.25 0.35 0.87 0.21 0.90 Pass 2 -2604.77 -2604.68 0.09 2.84 0.35 0.88 0.21 0.91 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 0.44 1.30 0.41 1.23 Pass 1 -2541.79 -2604.16 -62.37 2.03 0.39 1.15 0.24 1.10 Pass 2 -2604.16 -2603.89 0.27 2.99 0.38 1.16 0.24 1.11 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 0.62 1.43 0.51 1.23 Pass 1 -2155.28 -2604.76 -449.48 2.71 0.39 1.15 0.24 1.10 Pass 2 -2604.76 -2604.45 0.31 3.00 0.38 1.16 0.24 1.11 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.63 1.27 0.51 1.17 Pass 1 -2495.71 -2611.45 -115.74 2.10 0.47 1.35 0.49 1.16 WARNING: Serious failure in tn minimization dE = 1.488419238766255 Will revert to starting coordinates ... WARNING: Minimization may not be converged. Pass 2 -2611.45 -2613.80 -2.35 3.66 0.47 1.35 0.49 1.17 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.45 1.41 0.17 1.25 WARNING: Serious failure in tn minimization dE = 2.973011369704182 Will revert to starting coordinates ... Pass 1 -2539.13 -2608.94 -69.81 2.88 0.36 1.12 0.18 1.08 WARNING: Serious failure in tn minimization dE = 2.524191840650928 Will revert to starting coordinates ... WARNING: Minimization may not be converged. WARNING: sampling failure in side opt: 0.5244786272842248 (will revert to previous best ...) Pass 2 -2608.94 -2608.94 0.00 4.36 0.36 1.12 0.18 1.08 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 0.50 1.55 0.17 1.32 Pass 1 -2477.53 -2603.92 -126.39 2.38 0.36 1.06 0.18 1.03 Pass 2 -2603.92 -2603.80 0.12 2.87 0.36 1.06 0.18 1.03 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 0.41 1.46 0.34 1.26 Pass 1 -2479.47 -2601.44 -121.97 2.22 0.38 1.31 0.23 1.27 Pass 2 -2601.44 -2602.58 -1.14 3.01 0.38 1.17 0.23 1.12 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 0.48 1.52 0.20 1.27 Pass 1 -2319.95 -2604.03 -284.08 2.71 0.35 1.06 0.21 1.09 Pass 2 -2604.03 -2603.84 0.19 2.93 0.35 0.88 0.21 0.90 Results so far: 6 351 -2613.80 0.47 1.35 0.49 1.17 7 179 -2608.94 0.36 1.12 0.18 1.08 1 45 -2608.02 0.35 0.87 0.21 0.90 3 112 -2604.68 0.35 0.88 0.21 0.91 5 317 -2604.45 0.38 1.16 0.24 1.11 4 141 -2603.89 0.38 1.16 0.24 1.11 10 12 -2603.84 0.35 0.88 0.21 0.90 8 87 -2603.80 0.36 1.06 0.18 1.03 2 59 -2603.09 0.38 1.17 0.24 1.11 9 17 -2602.58 0.38 1.17 0.23 1.12 Initial Minimized Side Opt Final ENERGY -2522.277 0.000 0.000 -2613.798 Global, ba 0.627 0.000 0.000 0.472 Global, al 1.564 0.000 0.000 1.349 Local, N/C 0.696 0.000 0.000 0.489 Local, all 1.330 0.000 0.000 1.168 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_27:OD1 [No apparent H-bonds] _:ASP_27:OD2 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -35.80 179.33 _:ASN_42 -165.00 105.00 -173.28 _:GLY_43 70.89 84.81 -180.00 WARNING: above phi/psi not represented by library GLYback Actual angles 70.89 84.81 Closest rotamer 65.00 60.00 Delta -5.89 -24.81 _:VAL_44 -180.00 155.00 -180.00 _:ASP_45 -20.00 -85.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -20.00 -85.00 Closest rotamer -50.00 -60.00 Delta -30.00 25.00 _:GLY_46 170.00 -165.00 179.52 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.60 2.60 1 2.60 2.60 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.32 19 1.49 6.07 19 1.49 6.07 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.36 21 1.49 6.07 21 1.49 6.07 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.60 2.60 1 2.60 2.60 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.35 21 1.49 6.07 21 1.49 6.07 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.32 2.32 1 2.32 2.32 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.55 31 1.49 6.08 31 1.49 6.08 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.50 2.50 1 2.50 2.50 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.71 34 1.49 5.83 34 1.49 5.83 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 13 0.58 2.82 13 0.58 2.82 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.09 59 1.49 6.09 59 1.49 6.09 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 15 0.77 3.03 15 0.77 3.03 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.28 70 1.30 5.82 70 1.30 5.82 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 11 1.47 3.29 11 1.47 3.29 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.62 115 1.44 5.84 115 1.44 5.84 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 17 1.10 3.69 17 1.10 3.69 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 2.67 167 0.70 5.85 167 0.70 5.85 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 32 0.55 3.70 32 0.55 3.70 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 5.69 530 0.70 6.07 530 0.70 6.07 Number of closed loops found: 10 0.40 0.11 Results of loop screening 20.00 0.01 Loops NOT rejected 2 1.12 1.13 1.13 Loops rejected for theta 4 0.57 1.34 1.95 Loops rejected for phi/psi 4 1.25 1.61 2.13 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 1.0 2.0 2 Best loop that was rejected: 0.5704971444073115 failed theta test: 89.38594840953817 failed phi/psi test: 113.5705867482877 87.48875113636919 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 125034.608774 537.527518 171.902885 125744.039177 SGB 6502.596403 -2846.213998 -2414.533064 1241.849341 TOTAL 131537.205177 -2308.686480 -2242.630179 126985.888517 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 360.999956 167.753184 54601.413748 55130.166889 EL 2029.771128 -4425.858431 101.127663 -2294.959640 SGB -2414.533064 3050.575658 -130.458411 505.584183 TOTAL -23.761980 -1207.529589 54572.083001 53340.791431 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5094.833727 NONPOLAR 13.559947 SGB TOT -932.867140 SOLV TOT -919.307193 TOTALE 177659.939233 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 125034.608774 537.527518 171.902885 125744.039177 SGB 6502.596403 -2846.213998 -2414.533064 1241.849341 TOTAL 131537.205177 -2308.686480 -2242.630179 126985.888517 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 360.999956 167.753184 54601.413748 55130.166889 EL 2029.771128 -4425.858431 101.127663 -2294.959640 SGB -2414.533064 3050.575658 -130.458411 505.584183 TOTAL -23.761980 -1207.529589 54572.083001 53340.791431 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5094.833727 NONPOLAR 13.559947 SGB TOT -932.867140 SOLV TOT -919.307193 TOTALE 177659.939233 Summary for structure: INITIAL ENERGY 177659.939 Global, backbone 3.965 Global, all heavy at 4.349 Local, N/CA/C/O 3.728 Local, all heavy ato 4.219 Parameters for generating loops ... Minimum conformations: 64 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 32 0.55 3.70 32 0.55 3.70 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 5.70 530 0.70 6.07 530 0.70 6.07 Number of closed loops found: 10 0.40 0.11 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.11 109 0.47 3.48 109 0.47 3.48 Right branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 12.09 1680 0.73 6.10 1680 0.73 6.10 Number of closed loops found: 127 0.30 0.16 Results of loop screening 20.00 0.17 Loops NOT rejected 33 0.58 1.15 1.81 Loops rejected for theta 70 0.72 1.27 2.24 Loops rejected for phi/psi 21 0.58 1.02 1.46 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 1 1.67 1.67 1.67 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 2 0.81 1.17 1.52 Histogram of accepted loops: 0.0 1.0 11 1.0 2.0 22 Best loop that was rejected: 0.5807690816026239 failed phi/psi test: 106.0640105380797 85.94575220971133 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.18 337 0.60 3.73 337 0.60 3.73 Right branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 44.88 8418 0.68 6.17 8418 0.68 6.17 Number of closed loops found: 1523 0.20 0.43 Results of loop screening 20.00 2.11 Loops NOT rejected 467 0.58 1.18 2.18 Loops rejected for theta 759 0.57 1.35 2.53 Loops rejected for phi/psi 285 0.57 1.14 2.90 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 5 1.86 2.14 2.67 Loops rejected for L/R 3 1.27 1.29 1.31 Loops rejected for sidechn 4 1.07 1.24 1.34 Histogram of accepted loops: 0.0 1.0 126 1.0 2.0 339 2.0 3.0 2 Best loop that was rejected: 0.5679528692941411 failed theta test: 141.0319654055062 CLUSTERING PARAMETERS Number of data points: 467 Number of descriptors: 60 Number of clusters: 12 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.020 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 32 379 1.30 1.69 1.51 3.13 2 24 242 1.09 1.33 1.18 1.51 3 48 92 1.03 1.28 1.08 1.42 4 55 195 1.05 1.26 1.07 2.55 5 16 194 1.29 1.40 1.29 1.75 6 58 208 0.58 0.93 0.60 2.19 7 28 16 1.30 1.86 1.52 1.90 8 42 135 1.33 1.82 1.36 2.44 9 62 395 0.63 1.06 0.83 1.87 10 38 78 1.24 1.73 1.34 1.79 11 48 316 0.83 1.42 0.98 2.62 12 16 129 1.74 2.18 1.81 2.71 Data selected from clustering: 12 0.60 1.81 Big cluster found: 12 2.712245789029339 Clusters added; will try again ... Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 32 379 1.30 1.69 1.51 3.13 2 24 242 1.09 1.33 1.18 1.51 3 48 92 1.03 1.28 1.08 1.42 4 55 195 1.05 1.26 1.07 2.55 5 16 194 1.29 1.40 1.29 1.75 6 58 208 0.58 0.93 0.60 2.19 7 28 16 1.30 1.86 1.52 1.90 8 36 454 1.33 1.82 1.58 2.23 9 62 395 0.63 1.06 0.83 1.87 10 38 78 1.24 1.73 1.34 1.79 11 48 316 0.83 1.42 0.98 2.62 12 5 128 1.74 1.81 1.80 1.24 13 10 56 1.60 1.86 1.71 1.72 14 7 49 1.78 2.18 1.78 1.17 Data selected from clustering: 14 0.60 1.80 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 1.51 3.32 1.23 2.69 Pass 1 -2810.76 -2951.64 -140.88 4.42 1.12 2.38 0.94 1.99 Pass 2 -2951.64 -2952.11 -0.46 4.12 1.12 2.38 0.94 1.99 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 1.18 3.08 1.32 3.09 Pass 1 -2813.39 -2956.87 -143.48 3.35 1.26 2.66 1.19 2.60 WARNING: sampling failure in side opt: 0.6734385042350368 (will revert to previous best ...) Pass 2 -2956.87 -2956.87 0.00 5.10 1.26 2.66 1.19 2.60 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 1.08 3.03 1.25 2.98 Pass 1 -2788.70 -2953.50 -164.80 3.86 1.14 2.54 1.02 2.18 Pass 2 -2953.50 -2954.04 -0.54 6.70 1.13 2.49 0.96 2.10 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 1.07 2.95 1.16 2.72 Pass 1 -2765.54 -2955.01 -189.47 3.37 1.14 2.54 1.02 2.19 WARNING: sampling failure in side opt: 1.471223790176737 (will revert to previous best ...) Pass 2 -2955.01 -2955.01 0.00 6.72 1.14 2.54 1.02 2.19 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 1.29 2.99 1.29 2.71 Pass 1 -2810.27 -2955.08 -144.81 4.32 1.12 2.39 0.95 2.02 WARNING: sampling failure in side opt: 3.962783258020409 (will revert to previous best ...) Pass 2 -2955.08 -2955.08 0.00 6.02 1.12 2.39 0.95 2.02 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.60 1.43 0.43 1.48 WARNING: Serious failure in tn minimization dE = 3.531716849665827 Will revert to starting coordinates ... Pass 1 -2797.43 -2964.22 -166.78 5.00 0.76 1.77 0.58 1.48 WARNING: Serious failure in tn minimization dE = 2.186890524736555 Will revert to starting coordinates ... WARNING: Minimization may not be converged. WARNING: sampling failure in side opt: 2.779182799770297 (will revert to previous best ...) Pass 2 -2964.22 -2964.22 0.00 6.15 0.76 1.77 0.58 1.48 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 1.52 2.89 1.40 2.80 Pass 1 -2795.71 -2955.09 -159.39 3.30 1.26 2.66 1.19 2.60 Pass 2 -2955.09 -2955.50 -0.41 4.21 1.25 2.66 1.18 2.59 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 1.58 3.56 1.47 3.05 Pass 1 -2765.49 -2950.72 -185.23 3.84 1.44 3.22 1.35 2.72 Pass 2 -2950.72 -2950.34 0.38 4.18 1.44 3.22 1.35 2.72 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 0.83 1.99 0.50 1.57 Pass 1 -2838.37 -2960.03 -121.66 2.96 0.82 1.85 0.64 1.56 Pass 2 -2960.03 -2960.09 -0.07 3.29 0.81 1.85 0.64 1.56 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 1.34 2.91 1.42 2.88 Pass 1 -2717.68 -2944.58 -226.90 2.72 1.29 2.63 1.23 2.53 Pass 2 -2944.58 -2944.41 0.17 3.24 1.29 2.63 1.23 2.53 =================== Working on cluster 11 Summary of side chain addition/minim: Initial 0.98 2.17 0.83 1.96 Pass 1 -2763.76 -2954.05 -190.29 3.05 0.97 1.97 0.89 1.63 Pass 2 -2954.05 -2954.08 -0.02 4.23 0.97 1.97 0.89 1.63 =================== Working on cluster 12 Summary of side chain addition/minim: Initial 1.80 3.10 1.48 2.88 Pass 1 -2732.74 -2938.27 -205.53 3.09 2.33 3.31 1.45 2.54 Pass 2 -2938.27 -2938.37 -0.10 4.44 2.33 3.31 1.45 2.54 =================== Working on cluster 13 Summary of side chain addition/minim: Initial 1.71 3.06 1.55 2.86 Pass 1 -2799.53 -2941.93 -142.40 2.55 1.40 3.11 1.39 2.81 Pass 2 -2941.93 -2941.82 0.11 3.39 1.40 3.12 1.39 2.81 =================== Working on cluster 14 Summary of side chain addition/minim: Initial 1.78 2.57 1.33 2.60 Pass 1 -2861.04 -2963.48 -102.44 2.68 2.07 3.04 1.38 2.92 Pass 2 -2963.48 -2963.45 0.03 3.58 2.07 3.04 1.38 2.92 Results so far: 6 208 -2964.22 0.76 1.77 0.58 1.48 14 49 -2963.45 2.07 3.04 1.38 2.92 9 395 -2960.09 0.81 1.85 0.64 1.56 2 242 -2956.87 1.26 2.66 1.19 2.60 7 16 -2955.50 1.25 2.66 1.18 2.59 5 194 -2955.08 1.12 2.39 0.95 2.02 4 195 -2955.01 1.14 2.54 1.02 2.19 11 316 -2954.08 0.97 1.97 0.89 1.63 3 92 -2954.04 1.13 2.49 0.96 2.10 1 379 -2952.11 1.12 2.38 0.94 1.99 8 454 -2950.34 1.44 3.22 1.35 2.72 10 78 -2944.41 1.29 2.63 1.23 2.53 13 56 -2941.82 1.40 3.12 1.39 2.81 12 128 -2938.37 2.33 3.31 1.45 2.54 Initial Minimized Side Opt Final ENERGY 177659.939 0.000 0.000 -2964.220 Global, ba 3.965 0.000 0.000 0.765 Global, al 4.349 0.000 0.000 1.775 Local, N/C 3.728 0.000 0.000 0.582 Local, all 4.219 0.000 0.000 1.478 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_41:OD1 INTRA HBOND (side/side) _:ASP_41:OD2 _:GLN_37:NE2 1 2.695 [No apparent H-bonds] _:ASN_42:OD1 INTRA HBOND (side/main) _:ASN_42:ND2 _:TYR_38:O 1 2.768 INTRA HBOND (side/side) _:ASP_45:OD1 _:TRP_48:NE1 1 2.724 INTRA HBOND (side/main) _:ASP_45:OD1 _:GLY_46:N 1 2.952 [No apparent H-bonds] _:ASP_45:OD2 Summary of side chain addition/minim: Initial 1.08 1.40 0.61 1.11 Pass 1 -2916.22 -3017.23 -101.00 22.63 0.58 1.23 0.50 1.19 Pass 2 -3017.23 -3017.60 -0.38 20.90 0.58 1.23 0.50 1.20 =================== Working on cluster (HELIX) 4 shift (z): 0.85 trans (x): 0.17 trans (y): 0.21 yaw: -0.19 pitch: 0.20 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 -175.30 -168.90 _:ALA_28 -93.56 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 1 1.00 1.00 1 1.00 1.00 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 1.00 1.00 1 1.00 1.00 Number of closed loops found: 1 0.50 0.08 Results of loop screening 25.00 0.00 Loops NOT rejected 1 0.77 0.77 0.77 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 1 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 88.384856 99.624615 149.946223 337.955694 SGB 6364.886971 -2795.446536 -2413.569582 1155.870853 TOTAL 6453.271827 -2695.821921 -2263.623360 1493.826547 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 341.053233 -106.451307 -12.843169 221.758757 EL 2053.634434 -4454.117363 44.045736 -2356.437193 SGB -2413.569582 2970.914193 -57.647449 499.697162 TOTAL -18.881915 -1589.654478 -26.444882 -1634.981274 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4986.400569 NONPOLAR 22.540675 SGB TOT -917.262972 SOLV TOT -894.722297 TOTALE -2691.445039 Summary for structure: INITIAL ENERGY -2691.445 Global, backbone 0.771 Global, all heavy at 1.436 Local, N/CA/C/O 0.806 Local, all heavy ato 1.327 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -47.30 178.09 _:ASN_42 -82.92 9.85 173.51 _:GLY_43 75.63 21.99 -180.00 _:VAL_44 -180.00 105.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -180.00 105.00 Closest rotamer -165.00 105.00 Delta 15.00 0.00 _:ASP_45 -70.00 -105.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -70.00 -105.00 Closest rotamer -100.00 -95.00 Delta -30.00 10.00 _:GLY_46 -180.00 -175.00 179.52 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.81 2.81 1 2.81 2.81 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.35 16 2.02 6.03 16 2.02 6.03 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.43 18 2.01 6.05 18 2.01 6.05 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.81 2.81 1 2.81 2.81 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.43 18 2.01 6.05 18 2.01 6.05 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.77 2.77 1 2.77 2.77 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.57 20 1.69 6.04 20 1.69 6.04 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.78 2.78 1 2.78 2.78 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.81 38 0.81 6.03 38 0.81 6.03 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 15 0.55 3.57 15 0.55 3.57 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.18 49 1.22 6.17 49 1.22 6.17 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 12 0.57 2.65 12 0.57 2.65 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.45 67 0.97 6.04 67 0.97 6.04 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 12 0.76 2.97 12 0.76 2.97 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.67 102 1.61 6.28 102 1.61 6.28 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 23 0.71 3.45 23 0.71 3.45 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 2.95 163 1.06 6.30 163 1.06 6.30 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.09 40 0.56 3.57 40 0.56 3.57 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 6.37 449 0.91 6.29 449 0.91 6.29 Number of closed loops found: 5 0.40 0.11 Results of loop screening 25.00 0.01 Loops NOT rejected 2 1.13 1.14 1.15 Loops rejected for theta 1 1.14 1.14 1.14 Loops rejected for phi/psi 2 1.26 1.39 1.52 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 1.0 2.0 2 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 268.071994 199.591297 164.912345 632.575636 SGB 6420.278101 -2801.190884 -2452.648108 1166.439109 TOTAL 6688.350094 -2601.599587 -2287.735763 1799.014745 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 498.632968 -54.771504 -16.122107 427.739356 EL 2061.830560 -4492.626991 79.275736 -2351.520694 SGB -2452.648108 3046.653340 -90.274383 503.730849 TOTAL 107.815420 -1500.745155 -27.120754 -1420.050489 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5020.824245 NONPOLAR 30.880973 SGB TOT -898.006179 SOLV TOT -867.125205 TOTALE -2158.330907 Summary for structure: INITIAL ENERGY -2158.331 Global, backbone 1.143 Global, all heavy at 2.487 Local, N/CA/C/O 1.018 Local, all heavy ato 2.121 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -105.00 -70.00 -180.00 _:ASP_27 -75.00 105.00 178.23 _:ALA_28 -38.33 -23.89 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles -38.33 -23.89 Closest rotamer -45.00 -30.00 Delta -6.67 -6.11 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 0.92 0.92 1 0.92 0.92 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 1 0.92 0.92 1 0.92 0.92 Number of closed loops found: 1 0.50 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 1 0.70 0.70 0.70 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 1 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 267.996832 200.172783 165.140829 633.310444 SGB 6433.514825 -2820.495395 -2433.991831 1179.027599 TOTAL 6701.511657 -2620.322612 -2268.851002 1812.338044 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 498.636382 -143.731063 -13.075960 341.829360 EL 2061.895153 -4473.233789 67.204582 -2344.134054 SGB -2433.991831 3025.320173 -79.454740 511.873602 TOTAL 126.539705 -1591.644678 -25.326119 -1490.431092 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5023.968164 NONPOLAR 27.010292 SGB TOT -899.075131 SOLV TOT -872.064839 TOTALE -2241.059089 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 267.996832 200.172783 165.140829 633.310444 SGB 6433.514825 -2820.495395 -2433.991831 1179.027599 TOTAL 6701.511657 -2620.322612 -2268.851002 1812.338044 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 498.636382 -143.731063 -13.075960 341.829360 EL 2061.895153 -4473.233789 67.204582 -2344.134054 SGB -2433.991831 3025.320173 -79.454740 511.873602 TOTAL 126.539705 -1591.644678 -25.326119 -1490.431092 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5023.968164 NONPOLAR 27.010292 SGB TOT -899.075131 SOLV TOT -872.064839 TOTALE -2241.059089 Summary for structure: INITIAL ENERGY -2241.059 Global, backbone 0.771 Global, all heavy at 1.436 Local, N/CA/C/O 0.806 Local, all heavy ato 1.327 Parameters for generating loops ... Minimum conformations: 16 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 1 0.92 0.92 1 0.92 0.92 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.10 2 0.81 0.81 2 0.81 0.81 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.16 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.27 18 0.39 1.06 18 0.39 1.06 Number of closed loops found: 18 0.20 0.09 Results of loop screening 20.00 0.02 Loops NOT rejected 13 0.35 0.56 0.74 Loops rejected for theta 5 0.34 0.53 0.82 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 13 Best loop that was rejected: 0.3445631734265858 failed theta test: 135.9840786987356 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 2.04 977 0.33 1.18 977 0.33 1.18 Number of closed loops found: 977 0.10 0.13 Results of loop screening 20.00 1.46 Loops NOT rejected 739 0.26 0.46 0.83 Loops rejected for theta 223 0.31 0.48 0.84 Loops rejected for phi/psi 15 0.40 0.59 0.72 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 739 CLUSTERING PARAMETERS Number of data points: 739 Number of descriptors: 36 Number of clusters: 8 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.010 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 143 524 0.37 0.72 0.46 0.84 2 83 390 0.33 0.59 0.47 0.77 3 149 271 0.26 0.46 0.34 0.78 4 80 325 0.43 0.59 0.44 0.77 5 55 456 0.33 0.57 0.38 0.80 6 97 682 0.55 0.83 0.60 0.75 7 37 664 0.46 0.65 0.53 0.68 8 95 181 0.27 0.53 0.34 0.90 Data selected from clustering: 8 0.34 0.60 Big cluster found: 8 0.9041215041602809 Clusters added; will try again ... Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 143 524 0.37 0.72 0.46 0.84 2 81 390 0.33 0.59 0.47 0.77 3 128 267 0.26 0.46 0.34 0.75 4 56 325 0.43 0.59 0.44 0.62 5 47 456 0.33 0.57 0.38 0.70 6 97 682 0.55 0.83 0.60 0.75 7 37 664 0.46 0.65 0.53 0.68 8 68 179 0.32 0.53 0.36 0.77 9 24 27 0.34 0.45 0.35 0.64 10 58 45 0.26 0.45 0.29 0.76 Data selected from clustering: 10 0.29 0.60 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.46 1.23 0.48 1.19 Pass 1 -2352.04 -2411.88 -59.84 2.03 0.34 1.14 0.24 1.08 Pass 2 -2411.88 -2411.79 0.08 3.01 0.33 1.14 0.24 1.08 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 0.47 1.22 0.41 1.14 Pass 1 -2351.90 -2411.37 -59.47 1.96 0.33 1.15 0.23 1.09 Pass 2 -2411.37 -2411.51 -0.14 3.02 0.33 1.14 0.24 1.09 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 0.34 1.21 0.28 1.22 Pass 1 -2350.81 -2415.92 -65.11 2.07 0.31 0.82 0.22 0.84 Pass 2 -2415.92 -2416.16 -0.24 2.97 0.30 0.82 0.22 0.85 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 0.44 1.24 0.28 1.14 Pass 1 -2377.29 -2415.41 -38.12 1.77 0.31 0.81 0.22 0.84 Pass 2 -2415.41 -2415.55 -0.14 2.88 0.30 0.82 0.22 0.85 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 0.38 1.49 0.40 1.32 Pass 1 -2373.10 -2419.21 -46.12 2.18 0.39 1.32 0.44 1.15 Pass 2 -2419.21 -2419.51 -0.30 2.94 0.40 1.32 0.45 1.15 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.60 1.20 0.50 1.15 Pass 1 -2373.10 -2419.14 -46.04 1.95 0.40 1.32 0.45 1.15 Pass 2 -2419.14 -2419.40 -0.26 2.90 0.40 1.32 0.45 1.15 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.53 1.15 0.39 1.09 Pass 1 -2333.85 -2412.00 -78.15 2.04 0.40 1.21 0.42 1.09 Pass 2 -2412.00 -2411.98 0.02 2.82 0.40 1.21 0.42 1.09 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 0.36 1.44 0.18 1.26 Pass 1 -2380.22 -2418.40 -38.18 2.68 0.34 1.14 0.24 1.08 Pass 2 -2418.40 -2418.31 0.09 3.01 0.33 1.14 0.24 1.08 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 0.35 1.56 0.19 1.33 Pass 1 -2376.87 -2413.99 -37.12 2.32 0.33 1.14 0.24 1.08 Pass 2 -2413.99 -2413.96 0.03 2.92 0.33 1.14 0.24 1.09 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 0.29 1.38 0.26 1.22 Pass 1 -2387.22 -2420.07 -32.85 2.01 0.40 1.32 0.44 1.15 Pass 2 -2420.07 -2419.63 0.44 2.94 0.40 1.32 0.45 1.15 Results so far: 10 45 -2419.63 0.40 1.32 0.45 1.15 5 456 -2419.51 0.40 1.32 0.45 1.15 6 682 -2419.40 0.40 1.32 0.45 1.15 8 179 -2418.31 0.33 1.14 0.24 1.08 3 267 -2416.16 0.30 0.82 0.22 0.85 4 325 -2415.55 0.30 0.82 0.22 0.85 9 27 -2413.96 0.33 1.14 0.24 1.09 7 664 -2411.98 0.40 1.21 0.42 1.09 1 524 -2411.79 0.33 1.14 0.24 1.08 2 390 -2411.51 0.33 1.14 0.24 1.09 Initial Minimized Side Opt Final ENERGY -2241.059 0.000 0.000 -2419.635 Global, ba 0.771 0.000 0.000 0.396 Global, al 1.436 0.000 0.000 1.319 Local, N/C 0.806 0.000 0.000 0.448 Local, all 1.327 0.000 0.000 1.154 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_27:OD1 [No apparent H-bonds] _:ASP_27:OD2 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -47.30 178.09 _:ASN_42 -130.00 125.00 -179.93 _:GLY_43 63.73 -127.00 -180.00 _:VAL_44 -140.00 160.00 -180.00 _:ASP_45 -50.00 -80.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -50.00 -80.00 Closest rotamer -55.00 -65.00 Delta -5.00 15.00 _:GLY_46 170.00 -165.00 179.52 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.81 2.81 1 2.81 2.81 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.36 16 2.02 6.03 16 2.02 6.03 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.45 18 2.01 6.05 18 2.01 6.05 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.81 2.81 1 2.81 2.81 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.43 18 2.01 6.05 18 2.01 6.05 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.77 2.77 1 2.77 2.77 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.57 20 1.69 6.04 20 1.69 6.04 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 1 2.78 2.78 1 2.78 2.78 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.82 38 0.81 6.03 38 0.81 6.03 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 15 0.55 3.57 15 0.55 3.57 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.18 49 1.22 6.17 49 1.22 6.17 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 12 0.57 2.65 12 0.57 2.65 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.46 67 0.97 6.04 67 0.97 6.04 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 12 0.76 2.97 12 0.76 2.97 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.69 102 1.61 6.28 102 1.61 6.28 Number of closed loops found: 0 0.50 0.10 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 23 0.71 3.45 23 0.71 3.45 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 2.98 163 1.06 6.30 163 1.06 6.30 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.10 40 0.56 3.57 40 0.56 3.57 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 6.40 449 0.91 6.29 449 0.91 6.29 Number of closed loops found: 5 0.40 0.11 Results of loop screening 20.00 0.00 Loops NOT rejected 2 1.13 1.14 1.15 Loops rejected for theta 3 1.14 1.31 1.52 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 1.0 2.0 2 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 51386.547800 455.514663 156.804561 51998.867024 SGB 6460.037166 -2836.490842 -2395.587944 1227.958380 TOTAL 57846.584966 -2380.976178 -2238.783384 53226.825404 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 348.645573 58.134441 -12.624643 394.155371 EL 2021.278128 -4390.819713 68.321354 -2301.220231 SGB -2395.587944 2991.820081 -79.550786 516.681351 TOTAL -25.664243 -1340.865191 -23.854075 -1390.383508 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5057.195517 NONPOLAR 20.793177 SGB TOT -916.967841 SOLV TOT -896.174664 TOTALE 49195.627500 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 51386.547800 455.514663 156.804561 51998.867024 SGB 6460.037166 -2836.490842 -2395.587944 1227.958380 TOTAL 57846.584966 -2380.976178 -2238.783384 53226.825404 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 348.645573 58.134441 -12.624643 394.155371 EL 2021.278128 -4390.819713 68.321354 -2301.220231 SGB -2395.587944 2991.820081 -79.550786 516.681351 TOTAL -25.664243 -1340.865191 -23.854075 -1390.383508 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5057.195517 NONPOLAR 20.793177 SGB TOT -916.967841 SOLV TOT -896.174664 TOTALE 49195.627500 Summary for structure: INITIAL ENERGY 49195.627 Global, backbone 3.293 Global, all heavy at 3.947 Local, N/CA/C/O 2.807 Local, all heavy ato 3.446 Parameters for generating loops ... Minimum conformations: 64 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.09 40 0.56 3.57 40 0.56 3.57 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 6.40 449 0.91 6.29 449 0.91 6.29 Number of closed loops found: 5 0.40 0.11 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.12 111 0.33 3.32 111 0.33 3.32 Right branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 13.28 1529 0.73 6.30 1529 0.73 6.30 Number of closed loops found: 88 0.30 0.15 Results of loop screening 20.00 0.14 Loops NOT rejected 30 0.62 1.28 1.89 Loops rejected for theta 29 1.00 1.51 1.88 Loops rejected for phi/psi 28 0.51 1.32 1.79 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 1 1.62 1.62 1.62 Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 3 1.0 2.0 27 Best loop that was rejected: 0.5131144482695711 failed phi/psi test: 18.01165651826218 86.80593590828704 failed side test: _:VAL_44 0.5499999999999998 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.27 431 0.42 3.88 431 0.42 3.88 Right branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 47.60 7848 0.83 6.31 7848 0.83 6.31 Number of closed loops found: 1142 0.20 0.41 Results of loop screening 20.00 1.79 Loops NOT rejected 469 0.55 1.23 2.03 Loops rejected for theta 392 0.60 1.44 2.05 Loops rejected for phi/psi 251 0.60 1.24 1.98 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 2 1.13 1.22 1.32 Loops rejected for L/R 15 0.69 1.33 1.79 Loops rejected for sidechn 13 0.71 1.04 1.30 Histogram of accepted loops: 0.0 1.0 87 1.0 2.0 381 2.0 3.0 1 CLUSTERING PARAMETERS Number of data points: 469 Number of descriptors: 60 Number of clusters: 12 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.010 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 46 93 1.15 1.51 1.30 2.08 2 22 456 1.46 1.69 1.57 1.73 3 24 389 1.49 1.62 1.58 0.95 4 77 183 1.08 1.41 1.18 1.93 5 54 191 1.18 1.36 1.18 2.00 6 36 166 1.08 1.41 1.15 2.64 7 46 406 0.61 1.13 0.84 1.83 8 25 54 1.48 2.03 1.69 2.53 9 21 393 1.10 1.37 1.17 2.81 10 53 304 0.55 1.80 1.04 2.62 11 39 143 1.31 1.68 1.39 2.06 12 26 366 0.59 1.25 0.87 2.39 Data selected from clustering: 12 0.84 1.69 Big cluster found: 12 2.390813022584750 Clusters added; will try again ... Summary of cluster results; time = 0.010 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 38 175 1.26 1.56 1.30 1.90 2 22 456 1.46 1.69 1.57 1.73 3 28 359 1.30 1.62 1.58 1.45 4 76 183 1.08 1.41 1.18 1.95 5 62 191 1.09 1.36 1.18 2.10 6 22 166 1.08 1.41 1.15 1.87 7 46 423 0.66 1.13 0.86 1.91 8 23 54 1.54 2.03 1.69 2.43 9 32 342 1.08 1.38 1.10 3.02 10 42 200 0.85 1.68 1.01 1.77 11 39 143 1.31 1.68 1.39 2.06 12 18 365 0.87 1.25 0.89 2.05 13 4 132 1.74 1.80 1.80 0.32 14 17 371 0.55 0.75 0.65 2.10 Data selected from clustering: 14 0.65 1.80 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 1.30 2.91 1.39 2.81 Pass 1 -2762.31 -2937.86 -175.55 5.07 1.35 2.69 1.22 2.58 Pass 2 -2937.86 -2937.90 -0.05 4.18 1.35 2.69 1.22 2.58 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 1.57 3.32 1.37 2.72 Pass 1 -2789.33 -2927.28 -137.95 4.15 1.48 3.23 1.36 2.62 Pass 2 -2927.28 -2927.78 -0.51 4.07 1.48 3.23 1.36 2.62 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 1.58 3.40 1.29 2.81 Pass 1 -2814.50 -2930.98 -116.48 3.48 1.32 2.63 1.09 2.19 Pass 2 -2930.98 -2931.16 -0.17 4.19 1.27 2.62 1.08 2.19 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 1.18 2.95 1.33 2.90 WARNING: Serious failure in tn minimization dE = 3.302519474286328 Will revert to starting coordinates ... Pass 1 -2748.56 -2935.66 -187.10 5.67 1.23 2.57 1.01 2.16 WARNING: Serious failure in tn minimization dE = 2.178271004594535 Will revert to starting coordinates ... WARNING: Minimization may not be converged. WARNING: sampling failure in side opt: 1.137443664258626 (will revert to previous best ...) Pass 2 -2935.69 -2935.69 0.00 5.40 1.23 2.57 1.01 2.16 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 1.18 3.02 1.21 2.78 WARNING: Serious failure in tn minimization dE = 3.997206887062930 Will revert to starting coordinates ... Pass 1 -2722.98 -2934.05 -211.07 4.85 1.26 2.63 1.08 2.22 WARNING: Serious failure in tn minimization dE = 2.086651296723630 Will revert to starting coordinates ... WARNING: Minimization may not be converged. WARNING: sampling failure in side opt: 2.081881588520901 (will revert to previous best ...) Pass 2 -2934.06 -2934.06 0.00 4.96 1.26 2.63 1.08 2.22 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 1.15 2.30 1.23 2.40 Pass 1 -2802.10 -2924.30 -122.20 3.30 1.29 2.64 1.22 2.68 Pass 2 -2924.30 -2924.60 -0.29 3.37 1.30 2.63 1.22 2.66 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.86 2.02 0.45 1.53 Pass 1 -2739.28 -2958.61 -219.33 2.97 0.35 0.54 0.28 0.41 Pass 2 -2958.61 -2958.73 -0.12 3.39 0.35 0.54 0.29 0.41 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 1.69 2.87 1.40 2.86 Pass 1 -2785.39 -2936.66 -151.26 2.86 1.35 2.65 1.22 2.54 Pass 2 -2936.66 -2936.31 0.35 3.31 1.35 2.65 1.22 2.54 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 1.10 2.75 1.06 2.39 Pass 1 -2806.36 -2935.09 -128.73 4.12 1.20 2.65 1.15 2.58 WARNING: Serious failure in tn minimization dE = 2.414368415014451 Will revert to starting coordinates ... WARNING: Minimization may not be converged. Pass 2 -2935.09 -2937.52 -2.43 4.83 1.20 2.62 1.15 2.55 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 1.01 2.33 0.82 2.15 WARNING: Serious failure in tn minimization dE = 3.080498624700340 Will revert to starting coordinates ... Pass 1 -2512.52 -2939.64 -427.12 5.12 1.01 2.03 0.96 1.68 WARNING: sampling failure in side opt: 2.182017074814667 (will revert to previous best ...) Pass 2 -2939.64 -2939.64 0.00 4.98 1.01 2.03 0.96 1.68 =================== Working on cluster 11 Summary of side chain addition/minim: Initial 1.39 3.11 1.38 2.72 Pass 1 -2729.47 -2925.10 -195.62 3.42 1.37 3.09 1.32 2.69 Pass 2 -2925.10 -2925.09 0.01 3.48 1.37 3.08 1.32 2.69 =================== Working on cluster 12 Summary of side chain addition/minim: Initial 0.89 2.28 0.83 1.82 WARNING: Serious failure in tn minimization dE = 3.217815503279780 Will revert to starting coordinates ... Pass 1 -2838.75 -2942.79 -104.04 4.49 0.92 2.03 0.88 1.68 WARNING: Serious failure in tn minimization dE = 3.321239464250084 Will revert to starting coordinates ... WARNING: Minimization may not be converged. Pass 2 -2942.79 -2942.86 -0.08 4.86 0.92 2.00 0.88 1.65 =================== Working on cluster 13 Summary of side chain addition/minim: Initial 1.80 2.83 1.39 2.84 Pass 1 -2774.26 -2929.96 -155.70 2.73 1.97 3.06 1.43 2.91 Pass 2 -2929.96 -2929.64 0.31 3.45 1.97 3.06 1.43 2.91 =================== Working on cluster 14 Summary of side chain addition/minim: Initial 0.65 1.70 0.75 1.55 Pass 1 -2833.84 -2938.67 -104.83 4.23 1.01 1.98 0.95 1.62 Pass 2 -2938.67 -2938.61 0.06 4.39 1.01 1.98 0.95 1.62 Results so far: 7 423 -2958.73 0.35 0.54 0.29 0.41 12 365 -2942.86 0.92 2.00 0.88 1.65 10 200 -2939.64 1.01 2.03 0.96 1.68 14 371 -2938.61 1.01 1.98 0.95 1.62 1 175 -2937.90 1.35 2.69 1.22 2.58 9 342 -2937.52 1.20 2.62 1.15 2.55 8 54 -2936.31 1.35 2.65 1.22 2.54 4 183 -2935.69 1.23 2.57 1.01 2.16 5 191 -2934.06 1.26 2.63 1.08 2.22 3 359 -2931.16 1.27 2.62 1.08 2.19 13 132 -2929.64 1.97 3.06 1.43 2.91 2 456 -2927.78 1.48 3.23 1.36 2.62 11 143 -2925.09 1.37 3.08 1.32 2.69 6 166 -2924.60 1.30 2.63 1.22 2.66 Initial Minimized Side Opt Final ENERGY 49195.627 0.000 0.000 -2958.726 Global, ba 3.293 0.000 0.000 0.345 Global, al 3.947 0.000 0.000 0.535 Local, N/C 2.807 0.000 0.000 0.285 Local, all 3.446 0.000 0.000 0.409 H-bond contacts in current structure: INTRA HBOND (side/side) _:ASP_41:OD1 _:GLN_37:NE2 1 2.747 [No apparent H-bonds] _:ASP_41:OD2 [No apparent H-bonds] _:ASN_42:OD1 INTRA HBOND (side/main) _:ASN_42:ND2 _:TYR_38:O 1 2.772 [No apparent H-bonds] _:ASP_45:OD1 [No apparent H-bonds] _:ASP_45:OD2 Summary of side chain addition/minim: Initial 0.80 0.94 0.41 0.64 Pass 1 -2892.05 -3030.96 -138.92 27.35 0.28 0.92 0.35 0.91 WARNING: sampling failure in side opt: 0.6803343920337284 (will revert to previous best ...) Pass 2 -3030.96 -3030.96 0.00 31.02 0.28 0.92 0.35 0.91 =================== Working on cluster (HELIX) 5 shift (z): -1.79 trans (x): 1.06 trans (y): 0.90 yaw: 0.03 pitch: 0.13 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 -178.55 -174.72 _:ALA_28 -80.31 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.13 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.67 7 1.32 1.41 7 1.32 1.41 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.68 7 1.32 1.41 7 1.32 1.41 Number of closed loops found: 7 0.10 0.08 Results of loop screening 25.00 0.01 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 7 1.07 1.09 1.12 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.073605640586198 failed theta test: 146.2720195889048 failed phi/psi test: 10.36992447956123 -64.18884041148647 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 4.83 109 0.80 1.55 109 0.80 1.55 Number of closed loops found: 109 0.10 0.09 Results of loop screening 25.00 0.10 Loops NOT rejected 11 0.72 0.78 0.83 Loops rejected for theta 95 0.78 1.05 1.18 Loops rejected for phi/psi 3 0.73 0.74 0.74 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 11 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 85.833177 143.089352 143.536242 372.458771 SGB 6450.402360 -2827.478610 -2433.324311 1189.599439 TOTAL 6536.235537 -2684.389258 -2289.788069 1562.058210 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 338.635268 274047.170425 -13.155114 274372.650580 EL 2048.185389 -4419.028651 46.699024 -2324.144239 SGB -2433.324311 3007.041420 -59.459239 514.257870 TOTAL -46.503653 272635.183194 -25.915330 272562.764211 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5045.521504 NONPOLAR 16.480470 SGB TOT -908.339885 SOLV TOT -891.859414 TOTALE 271529.105698 Summary for structure: INITIAL ENERGY 271529.106 Global, backbone 1.082 Global, all heavy at 2.494 Local, N/CA/C/O 1.223 Local, all heavy ato 2.177 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -152.55 166.70 WARNING: above phi/psi not represented by library GENback Actual angles -60.32 -152.55 Closest rotamer -80.00 -170.00 Delta -19.68 -17.45 _:ASN_42 34.38 9.85 173.51 WARNING: above phi/psi not represented by library GENback Actual angles 34.38 9.85 Closest rotamer 55.00 20.00 Delta 20.62 10.15 _:GLY_43 75.63 21.99 -180.00 _:VAL_44 -170.00 -165.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -170.00 -165.00 Closest rotamer -165.00 -170.00 Delta 5.00 -5.00 _:ASP_45 -70.00 -85.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -70.00 -85.00 Closest rotamer -80.00 -75.00 Delta -10.00 10.00 _:GLY_46 -165.00 -150.00 179.52 WARNING: above phi/psi not represented by library GLYback Actual angles -165.00 -150.00 Closest rotamer -165.00 -145.00 Delta 0.00 5.00 Gamma turn in _:ASN_42 34.38 9.85 173.51 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 4 1.24 4.64 4 1.24 4.64 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.32 29 1.21 5.68 29 1.21 5.68 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 4 1.24 4.64 4 1.24 4.64 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.33 29 1.21 5.68 29 1.21 5.68 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 4 1.43 4.64 4 1.43 4.64 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.40 32 1.18 5.65 32 1.18 5.65 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 10 1.40 4.64 10 1.40 4.64 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.57 37 1.65 5.63 37 1.65 5.63 Number of closed loops found: 1 0.50 0.09 Results of loop screening 25.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 1 1.92 1.92 1.92 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.916692692394626 failed phi/psi test: -13.79470729052258 86.36912851453918 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 7 1.78 4.64 7 1.78 4.64 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.72 48 1.31 5.67 48 1.31 5.67 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 17 1.36 4.64 17 1.36 4.64 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.28 70 1.20 5.67 70 1.20 5.67 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 19 1.26 4.64 19 1.26 4.64 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.82 109 1.23 5.68 109 1.23 5.68 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.09 29 1.22 4.64 29 1.22 4.64 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.88 168 1.22 5.68 168 1.22 5.68 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.10 45 1.53 4.64 45 1.53 4.64 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 3.31 256 1.10 5.76 256 1.10 5.76 Number of closed loops found: 5 0.50 0.10 Results of loop screening 25.00 0.01 Loops NOT rejected 3 1.44 1.67 1.85 Loops rejected for theta 1 2.39 2.39 2.39 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 1 1.41 1.41 1.41 Histogram of accepted loops: 1.0 2.0 3 Best loop that was rejected: 1.407969271396815 failed side test: _:VAL_44 0.5999999999999998 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 85.062380 139.864730 162.885692 387.812803 SGB 6472.177078 -2820.749404 -2479.661706 1171.765968 TOTAL 6557.239459 -2680.884675 -2316.776013 1559.578771 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 367.784982 274160.056025 1451.027384 275978.868391 EL 2067.331085 -4420.663544 16.849051 -2336.483409 SGB -2479.661706 3001.163137 -27.395504 494.105927 TOTAL -44.545639 272740.555617 1440.480931 274136.490909 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5056.984842 NONPOLAR 20.655354 SGB TOT -911.451241 SOLV TOT -890.795887 TOTALE 273139.401898 Summary for structure: INITIAL ENERGY 273139.402 Global, backbone 1.408 Global, all heavy at 2.557 Local, N/CA/C/O 1.275 Local, all heavy ato 1.994 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -85.00 -70.00 -180.00 _:ASP_27 -150.00 -165.00 171.27 _:ALA_28 -40.17 -62.86 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles -40.17 -62.86 Closest rotamer -45.00 -55.00 Delta -4.83 7.86 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.15 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.85 11 0.89 1.41 11 0.89 1.41 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.83 11 0.89 1.41 11 0.89 1.41 Number of closed loops found: 11 0.10 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 11 0.75 1.05 1.11 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.7536195546696619 failed theta test: 137.1134190481783 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 6.40 311 0.70 1.55 311 0.70 1.55 Number of closed loops found: 311 0.10 0.10 Results of loop screening 20.00 0.27 Loops NOT rejected 11 0.68 0.72 0.82 Loops rejected for theta 300 0.68 0.98 1.18 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 11 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 83.178744 111.944170 169.138755 364.261669 SGB 6475.144939 -2836.155589 -2451.484156 1187.505193 TOTAL 6558.323683 -2724.211419 -2282.345402 1551.766862 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 367.724354 274245.757271 -12.917864 274600.563762 EL 2062.198867 -4389.532429 -4.397157 -2331.730719 SGB -2451.484156 2985.642824 -9.218650 524.940018 TOTAL -21.560935 272841.867667 -26.533671 272793.773061 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5067.638371 NONPOLAR 13.000182 SGB TOT -903.709004 SOLV TOT -890.708822 TOTALE 271742.385890 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 83.178744 111.944170 169.138755 364.261669 SGB 6475.144939 -2836.155589 -2451.484156 1187.505193 TOTAL 6558.323683 -2724.211419 -2282.345402 1551.766862 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 367.724354 274245.757271 -12.917864 274600.563762 EL 2062.198867 -4389.532429 -4.397157 -2331.730719 SGB -2451.484156 2985.642824 -9.218650 524.940018 TOTAL -21.560935 272841.867667 -26.533671 272793.773061 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5067.638371 NONPOLAR 13.000182 SGB TOT -903.709004 SOLV TOT -890.708822 TOTALE 271742.385890 Summary for structure: INITIAL ENERGY 271742.386 Global, backbone 0.827 Global, all heavy at 2.102 Local, N/CA/C/O 0.706 Local, all heavy ato 1.836 Parameters for generating loops ... Minimum conformations: 16 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 6.39 311 0.70 1.55 311 0.70 1.55 Number of closed loops found: 311 0.10 0.10 Results of loop screening 20.00 0.28 Loops NOT rejected 11 0.68 0.72 0.82 Loops rejected for theta 300 0.68 0.98 1.18 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 11 WARNING: both ofac_L and ofac_R bottomed out! CLUSTERING PARAMETERS Number of data points: 11 Number of descriptors: 36 Number of clusters: 8 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 2 7 0.74 0.79 0.79 0.18 2 3 10 0.70 0.71 0.71 0.13 3 1 1 0.70 0.70 0.70 0.00 4 1 4 0.68 0.68 0.68 0.00 5 1 3 0.68 0.68 0.68 0.00 6 1 5 0.68 0.68 0.68 0.00 7 1 2 0.68 0.68 0.68 0.00 8 1 6 0.82 0.82 0.82 0.00 Data selected from clustering: 8 0.68 0.82 =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.79 1.94 0.68 1.74 Pass 1 271727.45 271642.68 -84.77 2.71 0.83 1.64 0.84 1.50 Pass 2 271642.68 271643.01 0.33 2.85 0.83 1.64 0.84 1.51 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 0.71 1.84 0.65 1.70 Pass 1 271726.49 271642.52 -83.97 2.46 0.82 1.63 0.84 1.50 Pass 2 271642.52 271642.73 0.21 2.84 0.83 1.64 0.84 1.51 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 0.70 1.77 0.63 1.64 Pass 1 271742.51 271642.49 -100.02 2.66 0.82 1.63 0.84 1.50 Pass 2 271642.49 271642.43 -0.06 2.89 0.83 1.64 0.84 1.51 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 0.68 1.75 0.63 1.63 Pass 1 271733.75 271642.51 -91.24 2.62 0.82 1.63 0.84 1.50 Pass 2 271642.51 271642.52 0.01 2.92 0.83 1.64 0.84 1.51 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 0.68 1.75 0.63 1.64 Pass 1 271736.64 271642.41 -94.23 2.51 0.82 1.63 0.84 1.50 Pass 2 271642.41 271642.50 0.09 2.88 0.83 1.64 0.84 1.51 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.68 1.75 0.63 1.62 Pass 1 271732.66 271642.52 -90.14 2.62 0.82 1.63 0.84 1.50 Pass 2 271642.52 271642.58 0.06 2.88 0.83 1.64 0.84 1.51 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.68 1.76 0.63 1.63 Pass 1 271753.37 271641.66 -111.70 2.64 0.82 1.63 0.84 1.50 Pass 2 271641.66 271641.90 0.24 2.88 0.83 1.64 0.84 1.51 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 0.82 2.07 0.69 1.78 Pass 1 271779.85 271641.73 -138.12 2.62 0.83 1.64 0.84 1.50 Pass 2 271641.73 271641.67 -0.07 2.85 0.83 1.64 0.84 1.51 Results so far: 8 6 271641.66647430820 0.83 1.64 0.84 1.51 7 2 271641.89897017230 0.83 1.64 0.84 1.51 3 1 271642.42798810810 0.83 1.64 0.84 1.51 5 3 271642.49808748830 0.83 1.64 0.84 1.51 4 4 271642.52224158330 0.83 1.64 0.84 1.51 6 5 271642.58485075960 0.83 1.64 0.84 1.51 2 10 271642.72944294930 0.83 1.64 0.84 1.51 1 7 271643.01442800680 0.83 1.64 0.84 1.51 Initial Minimized Side Opt Final ENERGY 271742.386 0.000 0.000271641.666 Global, ba 0.827 0.000 0.000 0.827 Global, al 2.102 0.000 0.000 1.641 Local, N/C 0.706 0.000 0.000 0.839 Local, all 1.836 0.000 0.000 1.506 H-bond contacts in current structure: INTRA HBOND (side/main) _:ASP_27:OD1 _:ALA_28:N 1 2.736 [No apparent H-bonds] _:ASP_27:OD2 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -152.55 166.70 WARNING: above phi/psi not represented by library GENback Actual angles -60.32 -152.55 Closest rotamer -80.00 -170.00 Delta -19.68 -17.45 _:ASN_42 -100.00 20.00 175.84 _:GLY_43 -144.54 158.57 -180.00 WARNING: above phi/psi not represented by library GLYback Actual angles -144.54 158.57 Closest rotamer -150.00 160.00 Delta -5.46 1.43 _:VAL_44 -170.00 -165.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -170.00 -165.00 Closest rotamer -165.00 -170.00 Delta 5.00 -5.00 _:ASP_45 -70.00 -85.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -70.00 -85.00 Closest rotamer -80.00 -75.00 Delta -10.00 10.00 _:GLY_46 -165.00 -150.00 179.52 WARNING: above phi/psi not represented by library GLYback Actual angles -165.00 -150.00 Closest rotamer -165.00 -145.00 Delta 0.00 5.00 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 4 1.24 4.64 4 1.24 4.64 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.33 29 1.21 5.68 29 1.21 5.68 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 4 1.24 4.64 4 1.24 4.64 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.32 29 1.21 5.68 29 1.21 5.68 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 4 1.43 4.64 4 1.43 4.64 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.40 32 1.18 5.65 32 1.18 5.65 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 10 1.40 4.64 10 1.40 4.64 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.57 37 1.65 5.63 37 1.65 5.63 Number of closed loops found: 1 0.50 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 1 1.92 1.92 1.92 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.916692692394626 failed phi/psi test: -13.79470729052258 86.36912851453918 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 7 1.78 4.64 7 1.78 4.64 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.72 48 1.31 5.67 48 1.31 5.67 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 17 1.36 4.64 17 1.36 4.64 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.29 70 1.20 5.67 70 1.20 5.67 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 19 1.26 4.64 19 1.26 4.64 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.84 109 1.23 5.68 109 1.23 5.68 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.10 29 1.22 4.64 29 1.22 4.64 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.89 168 1.22 5.68 168 1.22 5.68 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.10 45 1.53 4.64 45 1.53 4.64 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 3.32 256 1.10 5.76 256 1.10 5.76 Number of closed loops found: 5 0.50 0.10 Results of loop screening 20.00 0.01 Loops NOT rejected 1 1.85 1.85 1.85 Loops rejected for theta 1 2.39 2.39 2.39 Loops rejected for phi/psi 1 1.44 1.44 1.44 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 1 1.71 1.71 1.71 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 1 1.41 1.41 1.41 Histogram of accepted loops: 1.0 2.0 1 Best loop that was rejected: 1.407969271396815 failed side test: _:VAL_44 0.5999999999999998 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 91807.193122 690.314696 175.170801 92672.678619 SGB 6441.404968 -2816.621301 -2421.464771 1203.318895 TOTAL 98248.598090 -2126.306605 -2246.293970 93875.997515 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 360.910674 315890.468807 -12.712135 316238.667347 EL 2022.983812 -4320.265758 34.337630 -2262.944316 SGB -2421.464771 2949.100617 -45.955408 481.680438 TOTAL -37.570285 314519.303667 -24.329913 314457.403469 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5038.524084 NONPOLAR 12.118758 SGB TOT -932.059979 SOLV TOT -919.941221 TOTALE 405728.460429 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 91807.193122 690.314696 175.170801 92672.678619 SGB 6441.404968 -2816.621301 -2421.464771 1203.318895 TOTAL 98248.598090 -2126.306605 -2246.293970 93875.997515 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 360.910674 315890.468807 -12.712135 316238.667347 EL 2022.983812 -4320.265758 34.337630 -2262.944316 SGB -2421.464771 2949.100617 -45.955408 481.680438 TOTAL -37.570285 314519.303667 -24.329913 314457.403469 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5038.524084 NONPOLAR 12.118758 SGB TOT -932.059979 SOLV TOT -919.941221 TOTALE 405728.460429 Summary for structure: INITIAL ENERGY 405728.460 Global, backbone 3.566 Global, all heavy at 4.110 Local, N/CA/C/O 3.308 Local, all heavy ato 4.016 Parameters for generating loops ... Minimum conformations: 64 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.10 45 1.53 4.64 45 1.53 4.64 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 3.33 256 1.10 5.76 256 1.10 5.76 Number of closed loops found: 5 0.50 0.10 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.16 83 1.07 4.64 83 1.07 4.64 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 7.68 846 1.02 5.68 846 1.02 5.68 Number of closed loops found: 56 0.40 0.12 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.24 197 1.08 4.88 197 1.08 4.88 Right branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 17.07 2697 0.68 5.69 2697 0.68 5.69 Number of closed loops found: 416 0.30 0.20 Results of loop screening 20.00 0.53 Loops NOT rejected 99 1.05 1.69 2.90 Loops rejected for theta 213 0.99 1.73 2.80 Loops rejected for phi/psi 90 0.97 1.67 2.41 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 2 1.75 1.88 2.01 Loops rejected for L/R 10 1.09 1.66 2.22 Loops rejected for sidechn 2 1.20 1.27 1.33 Histogram of accepted loops: 1.0 2.0 88 2.0 3.0 11 Best loop that was rejected: 0.9723634031598815 failed phi/psi test: 9.186996002305863 60.00131419878536 failed back test failed side test: _:VAL_44 0.6499999999999999 CLUSTERING PARAMETERS Number of data points: 99 Number of descriptors: 60 Number of clusters: 12 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.010 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 1 99 2.90 2.90 2.90 0.00 2 16 38 1.39 1.66 1.50 2.30 3 19 26 1.67 2.30 1.80 3.58 4 8 92 1.12 1.54 1.14 3.13 5 9 70 1.80 2.03 1.92 1.90 6 8 20 1.05 1.66 1.25 2.53 7 9 51 1.49 1.58 1.55 1.21 8 5 84 1.50 1.87 1.63 2.69 9 8 85 1.57 1.73 1.57 3.22 10 2 1 2.25 2.28 2.25 0.69 11 10 12 1.42 2.39 1.83 3.55 12 4 65 2.07 2.12 2.09 0.81 Data selected from clustering: 12 1.14 2.90 =================== Working on cluster 1 Summary of side chain addition/minim: Initial 2.90 4.63 1.36 3.36 Pass 1 271631.61 271404.08 -227.53 3.65 2.86 4.84 1.33 3.34 Pass 2 271404.08 271404.14 0.06 3.35 2.86 4.85 1.33 3.34 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 1.50 3.02 1.45 2.79 Pass 1 271602.07 271386.20 -215.87 3.56 1.69 3.14 1.35 2.59 Pass 2 271386.20 271386.06 -0.13 4.51 1.69 3.10 1.34 2.58 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 1.80 2.66 1.64 2.58 Pass 1 271541.54 271387.22 -154.32 3.29 1.80 2.63 1.51 2.50 Pass 2 271387.22 271376.76 -10.46 5.24 1.73 2.51 1.45 2.42 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 1.14 2.45 1.34 2.21 Pass 1 271505.57 271387.10 -118.46 4.34 1.30 1.97 1.42 1.76 Pass 2 271387.10 271387.57 0.47 3.83 1.29 1.97 1.42 1.77 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 1.92 2.85 1.68 2.65 Pass 1 271650.81 271397.43 -253.39 2.68 2.15 2.80 1.73 2.40 Pass 2 271397.43 271397.65 0.22 3.41 2.15 2.78 1.73 2.38 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 1.25 2.30 1.04 1.97 Pass 1 273223.88 271359.39 -1864.49 4.70 0.92 1.51 0.59 1.14 Pass 2 271359.39 271358.63 -0.76 3.70 0.92 1.51 0.59 1.14 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 1.55 2.82 1.50 2.59 Pass 1 271527.36 271403.22 -124.14 4.97 1.68 3.13 1.53 2.52 Pass 2 271403.22 271387.94 -15.28 8.63 1.64 3.16 1.39 2.61 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 1.63 2.95 1.79 2.90 Pass 1 271475.65 271386.94 -88.71 3.66 1.72 2.69 1.76 2.70 Pass 2 271386.94 271384.57 -2.38 5.59 1.63 2.63 1.65 2.68 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 1.57 3.05 1.71 3.02 Pass 1 271524.52 271389.63 -134.89 3.73 2.00 3.17 1.86 2.98 Pass 2 271389.63 271389.04 -0.58 3.38 1.99 3.17 1.86 2.98 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 2.25 2.60 1.50 2.66 Pass 1 271636.45 271384.30 -252.15 3.00 1.93 2.43 1.51 2.62 Pass 2 271384.30 271382.81 -1.49 4.60 1.92 2.43 1.51 2.61 =================== Working on cluster 11 Summary of side chain addition/minim: Initial 1.83 2.95 1.25 2.71 Pass 1 272062.51 271390.74 -671.78 4.78 1.35 2.10 0.92 1.62 Pass 2 271390.74 271384.73 -6.00 4.61 1.31 2.05 0.91 1.58 =================== Working on cluster 12 Summary of side chain addition/minim: Initial 2.09 3.33 1.73 2.92 WARNING: Serious failure in tn minimization dE = 1.531910650955979 Will revert to starting coordinates ... Pass 1 271534.66 271385.15 -149.51 5.41 1.95 3.00 1.68 2.66 WARNING: sampling failure in side opt: 4.065271414932795 (will revert to previous best ...) Pass 2 271385.15 271385.15 0.00 7.28 1.95 3.00 1.68 2.66 Results so far: 6 20 271358.62687903960 0.92 1.51 0.59 1.14 3 26 271376.76256067450 1.73 2.51 1.45 2.42 10 1 271382.80909156300 1.92 2.43 1.51 2.61 8 84 271384.56584586440 1.63 2.63 1.65 2.68 11 12 271384.73266018100 1.31 2.05 0.91 1.58 12 65 271385.15401635700 1.95 3.00 1.68 2.66 2 38 271386.06431158030 1.69 3.10 1.34 2.58 4 92 271387.57227410420 1.29 1.97 1.42 1.77 7 51 271387.93780794810 1.64 3.16 1.39 2.61 9 85 271389.04481833470 1.99 3.17 1.86 2.98 5 70 271397.64903583150 2.15 2.78 1.73 2.38 1 99 271404.14347182350 2.86 4.85 1.33 3.34 Initial Minimized Side Opt Final ENERGY 405728.460 0.000 0.000271358.627 Global, ba 3.566 0.000 0.000 0.921 Global, al 4.110 0.000 0.000 1.506 Local, N/C 3.308 0.000 0.000 0.592 Local, all 4.016 0.000 0.000 1.140 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_41:OD1 [No apparent H-bonds] _:ASP_41:OD2 [No apparent H-bonds] _:ASN_42:OD1 INTRA HBOND (side/main) _:ASN_42:ND2 _:TYR_38:O 1 2.820 [No apparent H-bonds] _:ASP_45:OD1 [No apparent H-bonds] _:ASP_45:OD2 Summary of side chain addition/minim: Initial 1.94 2.12 0.88 1.09 Pass 1 271427.37 -3039.46-274466.82 49.40 0.25 1.17 0.33 1.15 Pass 2 -3039.46 -3050.38 -10.92 33.11 0.26 0.96 0.32 0.95 =================== Working on cluster (HELIX) 6 shift (z): -1.51 trans (x): -0.75 trans (y): -0.05 yaw: 0.14 pitch: 0.07 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 163.70 -175.75 _:ALA_28 -60.54 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.04 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! Left branch (res,ofac,nstage): 120.00 60.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 0.05 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! WARNING: Could not close N-term loop shift (z): -1.23 trans (x): -0.20 trans (y): 0.29 yaw: 0.23 pitch: -0.10 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 175.80 -175.26 _:ALA_28 -73.71 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.15 5 0.42 0.66 5 0.42 0.66 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.14 5 0.42 0.66 5 0.42 0.66 Number of closed loops found: 5 0.30 0.09 Results of loop screening 25.00 0.00 Loops NOT rejected 3 0.30 0.39 0.56 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 2 0.50 0.50 0.50 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 3 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 83.949489 115.315058 163.681189 362.945735 SGB 6397.871989 -2807.483244 -2421.224921 1169.163824 TOTAL 6481.821478 -2692.168187 -2257.543733 1532.109559 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 337.153365 -30.128077 -12.674437 294.350851 EL 2056.136966 -4470.555993 111.496828 -2302.922200 SGB -2421.224921 3041.619215 -123.255804 497.138489 TOTAL -27.934591 -1459.064856 -24.433414 -1511.432860 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5006.541244 NONPOLAR 16.947717 SGB TOT -919.014010 SOLV TOT -902.066293 TOTALE -2547.691906 Summary for structure: INITIAL ENERGY -2547.692 Global, backbone 0.496 Global, all heavy at 1.744 Local, N/CA/C/O 0.761 Local, all heavy ato 1.630 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 4.68 -169.45 _:ASN_42 -145.39 9.85 173.51 WARNING: above phi/psi not represented by library GENback Actual angles -145.39 9.85 Closest rotamer -135.00 10.00 Delta 10.39 0.15 _:GLY_43 75.63 21.99 -180.00 _:VAL_44 -180.00 -180.00 -180.00 _:ASP_45 -30.00 -75.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -30.00 -75.00 Closest rotamer -50.00 -60.00 Delta -20.00 15.00 _:GLY_46 165.00 -145.00 179.52 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.58 2.58 1 2.58 2.58 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.40 25 0.98 5.76 25 0.98 5.76 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 1 2.58 2.58 1 2.58 2.58 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.40 25 0.98 5.76 25 0.98 5.76 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.04 2 2.62 2.80 2 2.62 2.80 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.42 27 0.96 5.67 27 0.96 5.67 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 2 2.62 2.80 2 2.62 2.80 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.60 31 0.97 5.68 31 0.97 5.68 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 3 2.62 2.80 3 2.62 2.80 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.82 57 1.02 5.67 57 1.02 5.67 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 14 0.42 2.62 14 0.42 2.62 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.22 86 0.77 5.66 86 0.77 5.66 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 14 0.61 2.63 14 0.61 2.63 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.61 113 0.58 5.76 113 0.58 5.76 Number of closed loops found: 1 0.50 0.09 Results of loop screening 25.00 0.00 Loops NOT rejected 1 1.12 1.12 1.12 Loops rejected for theta 0 N/A N/A N/A Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 1.0 2.0 1 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 84.962816 124.930005 165.448468 375.341289 SGB 6431.030791 -2811.595917 -2452.221819 1167.213056 TOTAL 6515.993607 -2686.665912 -2286.773350 1542.554345 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 359.192997 60.312725 -14.717949 404.787773 EL 2054.118947 -4445.261121 86.654529 -2304.487645 SGB -2452.221819 3013.609215 -98.097566 463.289830 TOTAL -38.909874 -1371.339182 -26.160985 -1436.410042 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5030.347116 NONPOLAR 21.997149 SGB TOT -947.622412 SOLV TOT -925.625262 TOTALE -2449.983845 Summary for structure: INITIAL ENERGY -2449.984 Global, backbone 1.119 Global, all heavy at 2.393 Local, N/CA/C/O 1.170 Local, all heavy ato 2.187 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -75.00 -30.00 -180.00 _:ASP_27 -170.00 -180.00 -171.98 _:ALA_28 -54.28 -51.87 -179.65 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 1 1.33 1.33 1 1.33 1.33 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 1 1.33 1.33 1 1.33 1.33 Number of closed loops found: 1 0.50 0.08 Results of loop screening 20.00 0.01 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 1 1.16 1.16 1.16 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.162013777206991 failed theta test: 83.29835234276709 failed phi/psi test: -175.9331899053838 -40.87554553507408 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.16 8 0.41 0.71 8 0.41 0.71 Number of closed loops found: 8 0.30 0.08 Results of loop screening 20.00 0.02 Loops NOT rejected 4 0.35 0.39 0.45 Loops rejected for theta 3 0.36 0.47 0.53 Loops rejected for phi/psi 1 0.57 0.57 0.57 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 4 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 84.324636 108.676553 156.170198 349.171387 SGB 6379.953000 -2802.565303 -2419.159351 1158.228347 TOTAL 6464.277636 -2693.888750 -2262.989153 1507.399733 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 365.693487 57.630304 -12.190786 411.133005 EL 2055.125335 -4462.079365 102.919342 -2304.034688 SGB -2419.159351 3041.199823 -114.882540 507.157932 TOTAL 1.659472 -1363.249239 -24.153984 -1385.743751 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4995.892136 NONPOLAR 17.073272 SGB TOT -911.346506 SOLV TOT -894.273234 TOTALE -2438.003530 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 84.324636 108.676553 156.170198 349.171387 SGB 6379.953000 -2802.565303 -2419.159351 1158.228347 TOTAL 6464.277636 -2693.888750 -2262.989153 1507.399733 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 365.693487 57.630304 -12.190786 411.133005 EL 2055.125335 -4462.079365 102.919342 -2304.034688 SGB -2419.159351 3041.199823 -114.882540 507.157932 TOTAL 1.659472 -1363.249239 -24.153984 -1385.743751 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4995.892136 NONPOLAR 17.073272 SGB TOT -911.346506 SOLV TOT -894.273234 TOTALE -2438.003530 Summary for structure: INITIAL ENERGY -2438.004 Global, backbone 0.313 Global, all heavy at 1.470 Local, N/CA/C/O 0.205 Local, all heavy ato 1.477 Parameters for generating loops ... Minimum conformations: 16 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.16 8 0.41 0.71 8 0.41 0.71 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.24 31 0.37 0.86 31 0.37 0.86 Number of closed loops found: 31 0.20 0.09 Results of loop screening 20.00 0.05 Loops NOT rejected 25 0.31 0.47 0.65 Loops rejected for theta 4 0.36 0.48 0.53 Loops rejected for phi/psi 2 0.49 0.50 0.50 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 25 CLUSTERING PARAMETERS Number of data points: 25 Number of descriptors: 36 Number of clusters: 8 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 3 8 0.38 0.42 0.41 0.18 2 3 5 0.36 0.37 0.37 0.21 3 5 16 0.44 0.54 0.53 0.80 4 1 7 0.36 0.36 0.36 0.00 5 2 12 0.35 0.36 0.36 0.10 6 4 20 0.62 0.65 0.64 0.35 7 4 24 0.54 0.59 0.58 0.32 8 3 2 0.31 0.36 0.35 0.24 Data selected from clustering: 8 0.35 0.64 =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.41 1.00 0.20 1.09 Pass 1 -2432.61 -2500.18 -67.57 2.37 0.28 1.13 0.14 1.14 Pass 2 -2500.18 -2500.18 0.00 2.90 0.28 1.13 0.14 1.14 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 0.37 1.17 0.14 1.24 Pass 1 -2428.16 -2498.39 -70.23 2.12 0.28 1.13 0.14 1.14 Pass 2 -2498.39 -2498.08 0.31 2.90 0.28 1.13 0.14 1.14 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 0.53 1.27 0.37 1.28 Pass 1 -2398.97 -2488.24 -89.27 2.40 0.29 1.26 0.15 1.29 Pass 2 -2488.24 -2488.90 -0.66 2.89 0.29 1.26 0.15 1.29 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 0.36 0.93 0.36 0.96 Pass 1 -2436.02 -2498.27 -62.25 2.38 0.28 1.13 0.14 1.14 Pass 2 -2498.27 -2498.22 0.05 2.89 0.28 1.13 0.14 1.14 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 0.36 0.96 0.37 1.02 Pass 1 -2446.69 -2498.94 -52.24 2.32 0.28 1.13 0.14 1.14 Pass 2 -2498.94 -2498.92 0.02 2.89 0.28 1.13 0.14 1.14 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.64 1.21 0.36 1.22 Pass 1 -2348.82 -2493.06 -144.24 2.12 0.29 1.28 0.15 1.31 Pass 2 -2493.06 -2493.60 -0.54 2.86 0.29 1.28 0.15 1.31 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.58 1.23 0.38 1.22 Pass 1 -2325.21 -2491.77 -166.55 2.08 0.29 1.29 0.15 1.31 Pass 2 -2491.77 -2492.74 -0.98 2.88 0.29 1.28 0.15 1.31 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 0.35 1.50 0.22 1.52 Pass 1 -2432.25 -2480.97 -48.72 2.30 0.29 1.26 0.15 1.29 Pass 2 -2480.97 -2480.92 0.04 2.93 0.29 1.26 0.15 1.29 Results so far: 1 8 -2500.18 0.28 1.13 0.14 1.14 5 12 -2498.92 0.28 1.13 0.14 1.14 4 7 -2498.22 0.28 1.13 0.14 1.14 2 5 -2498.08 0.28 1.13 0.14 1.14 6 20 -2493.60 0.29 1.28 0.15 1.31 7 24 -2492.74 0.29 1.28 0.15 1.31 3 16 -2488.90 0.29 1.26 0.15 1.29 8 2 -2480.92 0.29 1.26 0.15 1.29 Initial Minimized Side Opt Final ENERGY -2438.004 0.000 0.000 -2500.182 Global, ba 0.313 0.000 0.000 0.280 Global, al 1.470 0.000 0.000 1.131 Local, N/C 0.205 0.000 0.000 0.138 Local, all 1.477 0.000 0.000 1.141 H-bond contacts in current structure: INTRA HBOND (side/main) _:ASP_27:OD1 _:ALA_28:N 1 2.741 [No apparent H-bonds] _:ASP_27:OD2 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 4.68 -169.45 _:ASN_42 -65.00 -35.00 176.83 _:GLY_43 105.44 -32.21 -180.00 _:VAL_44 -160.00 -180.00 -180.00 _:ASP_45 -45.00 -70.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -45.00 -70.00 Closest rotamer -55.00 -65.00 Delta -10.00 5.00 _:GLY_46 160.00 -145.00 179.52 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.04 1 2.58 2.58 1 2.58 2.58 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.41 25 0.98 5.76 25 0.98 5.76 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.04 1 2.58 2.58 1 2.58 2.58 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.40 25 0.98 5.76 25 0.98 5.76 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 2 2.62 2.80 2 2.62 2.80 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.41 27 0.96 5.67 27 0.96 5.67 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 2 2.62 2.80 2 2.62 2.80 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.61 31 0.97 5.68 31 0.97 5.68 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.05 3 2.62 2.80 3 2.62 2.80 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.83 57 1.02 5.67 57 1.02 5.67 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 14 0.42 2.62 14 0.42 2.62 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.22 86 0.77 5.66 86 0.77 5.66 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 14 0.61 2.63 14 0.61 2.63 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.61 113 0.58 5.76 113 0.58 5.76 Number of closed loops found: 1 0.50 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 1 1.12 1.12 1.12 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.119036096589443 failed theta test: 134.4759501458262 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 13 1.03 2.91 13 1.03 2.91 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.89 164 0.53 5.66 164 0.53 5.66 Number of closed loops found: 2 0.50 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 1 1.15 1.15 1.15 Loops rejected for phi/psi 1 1.54 1.54 1.54 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.149568928400796 failed theta test: 153.3977989921841 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 27 0.85 3.91 27 0.85 3.91 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 3.15 295 0.70 5.75 295 0.70 5.75 Number of closed loops found: 0 0.50 0.10 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 47 0.55 3.91 47 0.55 3.91 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 7.21 794 0.59 5.77 794 0.59 5.77 Number of closed loops found: 27 0.40 0.11 Results of loop screening 20.00 0.04 Loops NOT rejected 6 0.56 1.31 1.84 Loops rejected for theta 13 0.95 1.43 1.71 Loops rejected for phi/psi 7 0.69 1.29 1.80 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 1 2.24 2.24 2.24 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 1 1.0 2.0 5 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 63390.868963 635.187916 162.800027 64188.856907 SGB 6428.762816 -2820.503304 -2409.108164 1199.151348 TOTAL 69819.631779 -2185.315388 -2246.308137 65388.008254 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 355.492599 5350.053523 -12.362970 5693.183152 EL 2027.765015 -4386.571783 85.444961 -2273.361807 SGB -2409.108164 2963.859094 -96.260554 458.490376 TOTAL -25.850551 3927.340835 -23.178563 3878.311721 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5033.497051 NONPOLAR 15.574805 SGB TOT -966.747164 SOLV TOT -951.172359 TOTALE 66657.505893 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 63390.868963 635.187916 162.800027 64188.856907 SGB 6428.762816 -2820.503304 -2409.108164 1199.151348 TOTAL 69819.631779 -2185.315388 -2246.308137 65388.008254 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 355.492599 5350.053523 -12.362970 5693.183152 EL 2027.765015 -4386.571783 85.444961 -2273.361807 SGB -2409.108164 2963.859094 -96.260554 458.490376 TOTAL -25.850551 3927.340835 -23.178563 3878.311721 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5033.497051 NONPOLAR 15.574805 SGB TOT -966.747164 SOLV TOT -951.172359 TOTALE 66657.505893 Summary for structure: INITIAL ENERGY 66657.506 Global, backbone 3.240 Global, all heavy at 3.900 Local, N/CA/C/O 2.817 Local, all heavy ato 3.670 Parameters for generating loops ... Minimum conformations: 64 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 47 0.55 3.91 47 0.55 3.91 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 7.22 794 0.59 5.77 794 0.59 5.77 Number of closed loops found: 27 0.40 0.11 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.13 126 0.42 3.56 126 0.42 3.56 Right branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 15.29 2496 0.47 5.76 2496 0.47 5.76 Number of closed loops found: 249 0.30 0.19 Results of loop screening 20.00 0.34 Loops NOT rejected 62 0.41 1.15 2.61 Loops rejected for theta 128 0.62 1.33 2.56 Loops rejected for phi/psi 53 0.47 1.22 2.64 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 1 2.29 2.29 2.29 Loops rejected for L/R 2 1.19 1.33 1.47 Loops rejected for sidechn 3 0.41 0.88 1.12 Histogram of accepted loops: 0.0 1.0 21 1.0 2.0 40 2.0 3.0 1 Best loop that was rejected: 0.4071089417296658 failed side test: _:VAL_44 0.6499999999999999 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.28 494 0.42 3.91 494 0.42 3.91 Right branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 56.53 12925 0.26 5.76 12925 0.26 5.76 Number of closed loops found: 5421 0.20 0.64 Results of loop screening 20.00 7.92 Loops NOT rejected 1582 0.31 1.14 2.55 Loops rejected for theta 2560 0.39 1.25 2.68 Loops rejected for phi/psi 1050 0.41 1.15 2.92 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 75 1.03 1.77 2.49 Loops rejected for L/R 50 0.47 0.96 1.51 Loops rejected for sidechn 104 0.41 1.08 1.75 Histogram of accepted loops: 0.0 1.0 542 1.0 2.0 1019 2.0 3.0 21 CLUSTERING PARAMETERS Number of data points: 1582 Number of descriptors: 60 Number of clusters: 12 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.060 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 137 1002 0.35 1.05 0.45 2.05 2 73 1489 0.77 1.36 0.95 2.76 3 184 666 0.68 1.34 0.94 2.37 4 45 88 1.09 2.55 1.60 3.76 5 208 55 0.75 1.72 1.14 2.85 6 147 907 0.31 1.08 0.48 2.49 7 71 375 1.23 1.59 1.37 2.73 8 92 1532 0.97 1.59 1.19 2.55 9 289 529 0.95 1.65 1.19 2.66 10 95 1481 0.53 1.29 0.80 2.66 11 112 774 1.33 1.84 1.48 3.12 12 129 1301 1.13 2.02 1.54 3.53 Data selected from clustering: 12 0.45 1.60 Big cluster found: 12 3.527428389725774 Clusters added; will try again ... Summary of cluster results; time = 0.050 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 160 1002 0.31 1.05 0.45 2.09 2 78 1489 0.68 1.36 0.95 2.77 3 215 666 0.68 1.34 0.94 2.50 4 45 88 1.09 2.55 1.60 3.76 5 168 56 0.84 1.72 1.18 2.74 6 126 907 0.40 1.09 0.48 2.52 7 71 375 1.23 1.59 1.37 2.73 8 92 1532 0.97 1.59 1.19 2.55 9 289 529 0.95 1.65 1.19 2.66 10 95 1481 0.53 1.29 0.80 2.66 11 89 768 1.33 1.77 1.47 2.64 12 93 1187 1.38 2.02 1.58 2.85 13 15 791 0.97 1.61 1.46 2.12 14 46 1272 1.13 1.83 1.50 2.50 Data selected from clustering: 14 0.45 1.60 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.45 1.31 0.48 1.25 Pass 1 -2588.71 -2707.56 -118.85 2.74 0.60 1.29 0.45 1.18 Pass 2 -2707.56 -2707.53 0.03 3.40 0.59 1.28 0.45 1.18 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 0.95 2.64 0.86 2.32 Pass 1********** -2689.58********** 4.01 0.82 2.01 0.81 1.80 Pass 2 -2689.58 -2689.25 0.33 3.49 0.81 2.00 0.80 1.80 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 0.94 1.92 0.74 1.80 Pass 1 -2604.21 -2675.13 -70.92 3.59 0.81 1.88 0.80 1.73 Pass 2 -2675.13 -2676.41 -1.27 4.25 0.81 1.88 0.80 1.73 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 1.60 2.21 1.17 2.34 Pass 1 -2547.87 -2690.46 -142.59 3.42 1.49 2.33 1.20 2.59 Pass 2 -2690.46 -2690.51 -0.05 3.49 1.49 2.33 1.20 2.59 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 1.18 2.18 0.78 1.98 Pass 1 -2554.69 -2709.00 -154.31 4.98 0.59 1.28 0.45 1.18 WARNING: sampling failure in side opt: 0.5035016113974962 (will revert to previous best ...) Pass 2 -2709.00 -2709.00 0.00 4.12 0.59 1.28 0.45 1.18 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.48 1.37 0.34 1.36 Pass 1 -2513.68 -2708.09 -194.41 2.46 0.57 1.20 0.43 1.10 Pass 2 -2708.09 -2708.20 -0.11 3.45 0.57 1.20 0.43 1.10 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 1.37 2.98 1.54 2.94 Pass 1 -2561.47 -2655.07 -93.60 2.68 1.44 2.97 1.42 2.74 Pass 2 -2655.07 -2656.32 -1.25 4.48 1.45 3.05 1.41 2.76 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 1.19 3.16 1.06 2.73 WARNING: Serious failure in tn minimization dE = 1.565307100187056 Will revert to starting coordinates ... Pass 1 -2545.55 -2665.56 -120.01 3.25 1.21 2.74 1.07 2.31 WARNING: sampling failure in side opt: 1.571648290262601 (will revert to previous best ...) Pass 2 -2665.55 -2665.55 0.00 4.93 1.21 2.74 1.07 2.31 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 1.19 2.93 1.31 2.92 Pass 1 -2527.04 -2663.38 -136.34 2.92 1.17 2.58 1.19 2.40 Pass 2 -2663.38 -2664.62 -1.24 5.01 1.17 2.58 1.19 2.40 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 0.80 1.98 0.56 1.53 Pass 1 -2562.76 -2692.48 -129.72 3.07 0.60 0.99 0.45 0.84 Pass 2 -2692.48 -2692.29 0.19 3.52 0.60 0.99 0.45 0.84 =================== Working on cluster 11 Summary of side chain addition/minim: Initial 1.47 2.54 1.57 2.75 Pass 1 -2574.57 -2666.93 -92.36 3.43 1.48 2.27 1.47 2.51 Pass 2 -2666.93 -2667.43 -0.50 3.60 1.48 2.25 1.47 2.48 =================== Working on cluster 12 Summary of side chain addition/minim: Initial 1.58 3.06 1.59 2.98 Pass 1 -2523.35 -2664.41 -141.06 2.71 1.66 2.94 1.57 2.76 Pass 2 -2664.41 -2664.38 0.03 3.56 1.66 2.95 1.57 2.77 =================== Working on cluster 13 Summary of side chain addition/minim: Initial 1.46 2.75 1.48 2.75 WARNING: Serious failure in tn minimization dE = 1.504624086981948 Will revert to starting coordinates ... Pass 1 -2455.80 -2663.78 -207.98 4.24 1.42 2.48 1.38 2.46 WARNING: sampling failure in side opt: 2.188767052141884 (will revert to previous best ...) Pass 2 -2663.77 -2663.77 0.00 4.93 1.42 2.48 1.38 2.46 =================== Working on cluster 14 Summary of side chain addition/minim: Initial 1.50 2.94 1.46 2.90 Pass 1 -2584.19 -2663.13 -78.94 2.63 1.42 2.48 1.38 2.47 Pass 2 -2663.13 -2662.66 0.47 3.39 1.42 2.48 1.38 2.47 Results so far: 5 56 -2709.00 0.59 1.28 0.45 1.18 6 907 -2708.20 0.57 1.20 0.43 1.10 1 1002 -2707.53 0.59 1.28 0.45 1.18 10 1481 -2692.29 0.60 0.99 0.45 0.84 4 88 -2690.51 1.49 2.33 1.20 2.59 2 1489 -2689.25 0.81 2.00 0.80 1.80 3 666 -2676.41 0.81 1.88 0.80 1.73 11 768 -2667.43 1.48 2.25 1.47 2.48 8 1532 -2665.55 1.21 2.74 1.07 2.31 9 529 -2664.62 1.17 2.58 1.19 2.40 12 1187 -2664.38 1.66 2.95 1.57 2.77 13 791 -2663.77 1.42 2.48 1.38 2.46 14 1272 -2662.66 1.42 2.48 1.38 2.47 7 375 -2656.32 1.45 3.05 1.41 2.76 Initial Minimized Side Opt Final ENERGY 66657.506 0.000 0.000 -2708.998 Global, ba 3.240 0.000 0.000 0.590 Global, al 3.900 0.000 0.000 1.278 Local, N/C 2.817 0.000 0.000 0.447 Local, all 3.670 0.000 0.000 1.176 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_41:OD1 [No apparent H-bonds] _:ASP_41:OD2 [No apparent H-bonds] _:ASN_42:OD1 INTRA HBOND (side/main) _:ASN_42:ND2 _:TYR_38:O 1 2.768 [No apparent H-bonds] _:ASP_45:OD1 [No apparent H-bonds] _:ASP_45:OD2 Summary of side chain addition/minim: Initial 1.13 1.31 0.55 0.84 WARNING: Serious failure in tn minimization dE = 2.400962023805732 Will revert to starting coordinates ... Pass 1 -2638.15 -3045.54 -407.39 28.87 0.27 1.10 0.27 1.10 Pass 2 -3045.54 -3045.53 0.01 50.17 0.28 1.04 0.27 1.02 =================== Working on cluster (HELIX) 7 shift (z): -2.49 trans (x): 1.11 trans (y): 1.40 yaw: 0.02 pitch: -0.04 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 -173.22 -174.26 _:ALA_28 -84.65 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.57 7 1.51 1.60 7 1.51 1.60 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.58 7 1.51 1.60 7 1.51 1.60 Number of closed loops found: 7 0.10 0.09 Results of loop screening 25.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 7 1.26 1.28 1.30 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.262512010517300 failed theta test: 146.6163395870234 failed phi/psi test: 14.53055171020864 -80.84208928615652 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 3.66 70 1.18 1.69 70 1.18 1.69 Number of closed loops found: 70 0.10 0.09 Results of loop screening 25.00 0.06 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 70 1.02 1.28 1.33 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.017596867530386 failed theta test: 137.4735543307303 failed phi/psi test: -13.72407030739549 -81.25069096626754 Left branch (res,ofac,nstage): 5.00 5.00 0.675 1 Stage: 1 _:ALA_25 _:ALA_28 4.22 84 1.18 1.69 84 1.18 1.69 Number of closed loops found: 84 0.10 0.09 Results of loop screening 25.00 0.08 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 84 1.02 1.28 1.34 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.017596867530386 failed theta test: 137.4735543307303 failed phi/psi test: -13.72407030739549 -81.25069096626754 Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 4.70 94 1.18 1.75 94 1.18 1.75 Number of closed loops found: 94 0.10 0.09 Results of loop screening 25.00 0.08 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 94 1.02 1.29 1.37 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.017596867530386 failed theta test: 137.4735543307303 failed phi/psi test: -13.72407030739549 -81.25069096626754 WARNING: both ofac_L and ofac_R bottomed out! COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 89.912035 114.309608 156.957745 361.179387 SGB 6505.198919 -2839.557496 -2453.338290 1212.303132 TOTAL 6595.110953 -2725.247888 -2296.380545 1573.482519 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 340.566958 *************** -13.179057 *************** EL 2051.371855 -4516.262130 146.193059 -2318.697216 SGB -2453.338290 3120.633809 -157.111217 510.184302 TOTAL -61.399476 *************** -24.097215 *************** TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5091.110579 NONPOLAR 15.402454 SGB TOT -915.284854 SOLV TOT -899.882400 TOTALE *************** Summary for structure: INITIAL ENERGY ********** Global, backbone 1.018 Global, all heavy at 2.243 Local, N/CA/C/O 0.851 Local, all heavy ato 1.994 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 5.00 5.00 0.650 1 Stage: 1 _:ALA_25 _:ALA_28 4.70 94 1.18 1.75 94 1.18 1.75 Number of closed loops found: 94 0.10 0.09 Results of loop screening 25.00 0.08 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 94 1.02 1.29 1.37 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.017596867530386 failed theta test: 137.4735543307303 failed phi/psi test: -13.72407030739549 -81.25069096626754 WARNING: both ofac_L and ofac_R bottomed out! WARNING: Could not close N-term loop shift (z): -2.31 trans (x): 0.69 trans (y): 1.20 yaw: 0.11 pitch: 0.03 roll: 0.00 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -74.00 -24.07 -177.76 _:ASP_27 -154.52 -173.53 -174.22 _:ALA_28 -84.12 -32.87 -179.65 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.09 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.17 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.21 58 0.94 1.81 58 0.94 1.81 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.21 58 0.94 1.81 58 0.94 1.81 Number of closed loops found: 58 0.10 0.09 Results of loop screening 25.00 0.05 Loops NOT rejected 4 0.82 0.84 0.86 Loops rejected for theta 50 0.83 1.23 1.36 Loops rejected for phi/psi 4 0.83 0.85 0.86 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 4 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 91.218372 146.550500 157.336199 395.105071 SGB 6494.915501 -2836.218858 -2450.924171 1207.772472 TOTAL 6586.133873 -2689.668358 -2293.587973 1602.877542 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 339.182950 165354.035992 -12.929402 165680.289541 EL 2052.100184 -4483.693622 123.700534 -2307.892904 SGB -2450.924171 3123.944512 -134.944439 538.075902 TOTAL -59.641037 163994.286883 -24.173307 163910.472538 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5083.125662 NONPOLAR 14.713861 SGB TOT -886.353117 SOLV TOT -871.639256 TOTALE 162895.862451 Summary for structure: INITIAL ENERGY 162895.862 Global, backbone 1.209 Global, all heavy at 2.711 Local, N/CA/C/O 1.350 Local, all heavy ato 2.349 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -162.12 162.59 WARNING: above phi/psi not represented by library GENback Actual angles -60.32 -162.12 Closest rotamer -75.00 -175.00 Delta -14.68 -12.88 _:ASN_42 48.38 9.85 173.51 WARNING: above phi/psi not represented by library GENback Actual angles 48.38 9.85 Closest rotamer 60.00 10.00 Delta 11.62 0.15 _:GLY_43 75.63 21.99 -180.00 _:VAL_44 -180.00 -170.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -180.00 -170.00 Closest rotamer -175.00 -180.00 Delta 5.00 -10.00 _:ASP_45 -60.00 -85.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -60.00 -85.00 Closest rotamer -55.00 -65.00 Delta 5.00 20.00 _:GLY_46 -170.00 -145.00 179.52 WARNING: above phi/psi not represented by library GLYback Actual angles -170.00 -145.00 Closest rotamer -165.00 -145.00 Delta 5.00 0.00 Gamma turn in _:ASN_42 48.38 9.85 173.51 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 6 1.25 4.58 6 1.25 4.58 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.33 30 0.76 5.50 30 0.76 5.50 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 6 1.25 4.58 6 1.25 4.58 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.33 30 0.76 5.50 30 0.76 5.50 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 6 1.42 4.58 6 1.42 4.58 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.38 33 0.76 5.55 33 0.76 5.55 Number of closed loops found: 0 0.50 0.08 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 10 1.41 4.58 10 1.41 4.58 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.57 40 0.76 5.55 40 0.76 5.55 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 9 1.79 4.58 9 1.79 4.58 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.72 58 0.76 5.53 58 0.76 5.53 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 16 1.58 4.58 16 1.58 4.58 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.20 96 0.76 5.53 96 0.76 5.53 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 18 1.26 4.58 18 1.26 4.58 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.71 146 0.76 5.54 146 0.76 5.54 Number of closed loops found: 2 0.50 0.10 Results of loop screening 25.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 1 1.24 1.24 1.24 Loops rejected for phi/psi 1 1.98 1.98 1.98 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.241068214423228 failed theta test: 156.1131588734824 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.09 29 1.42 4.58 29 1.42 4.58 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.84 197 0.76 5.55 197 0.76 5.55 Number of closed loops found: 0 0.50 0.10 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.11 50 1.45 4.76 50 1.45 4.76 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 3.34 349 0.76 5.66 349 0.76 5.66 Number of closed loops found: 12 0.50 0.10 Results of loop screening 25.00 0.02 Loops NOT rejected 6 1.33 1.66 2.32 Loops rejected for theta 3 1.44 2.21 2.74 Loops rejected for phi/psi 3 1.28 1.84 2.42 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 1.0 2.0 5 2.0 3.0 1 Best loop that was rejected: 1.280460929406113 failed phi/psi test: -16.21071789901504 90.53300894897838 failed back test failed side test: _:VAL_44 0.5999999999999998 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 100.798311 153.210288 163.731957 417.740556 SGB 6519.967102 -2836.495614 -2494.953241 1188.518247 TOTAL 6620.765413 -2683.285326 -2331.221283 1606.258804 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 410.464762 165858.224264 451.097660 166719.786686 EL 2062.696548 -4451.917779 63.978563 -2325.242668 SGB -2494.953241 3055.902715 -71.720560 489.228914 TOTAL -21.791931 164462.209201 443.355662 164883.772932 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5097.952105 NONPOLAR 20.921862 SGB TOT -925.251703 SOLV TOT -904.329841 TOTALE 163907.954733 Summary for structure: INITIAL ENERGY 163907.955 Global, backbone 1.280 Global, all heavy at 2.413 Local, N/CA/C/O 1.060 Local, all heavy ato 2.026 ============================================ Now working on new loop ... ============================================ _:ALA_25 _:ALA_28 4 Starting loop conformation: _:ALA_25 -155.57 161.45 176.75 _:VAL_26 -85.00 -60.00 -180.00 _:ASP_27 -165.00 -170.00 172.27 _:ALA_28 -29.86 -72.41 -179.65 WARNING: above phi/psi not represented by library GENback Actual angles -29.86 -72.41 Closest rotamer -45.00 -55.00 Delta -15.14 17.41 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:ALA_28 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop not split: forward generation. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 0.19 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.43 79 0.89 1.89 79 0.89 1.89 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 1.40 79 0.89 1.89 79 0.89 1.89 Number of closed loops found: 79 0.10 0.09 Results of loop screening 20.00 0.07 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 79 0.77 1.13 1.40 Loops rejected for phi/psi 0 N/A N/A N/A Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 0.7696695717854423 failed theta test: 137.4986528542546 failed phi/psi test: -9.910062517390372 -65.12253282431260 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 Stage: 1 _:ALA_25 _:ALA_28 11.90 1464 0.72 1.89 1464 0.72 1.89 Number of closed loops found: 1464 0.10 0.15 Results of loop screening 20.00 1.29 Loops NOT rejected 48 0.74 0.77 0.90 Loops rejected for theta 1414 0.70 1.19 1.40 Loops rejected for phi/psi 2 1.06 1.07 1.09 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 0.0 1.0 48 Best loop that was rejected: 0.7047238652339681 failed theta test: 132.1516461509743 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 92.526518 119.133689 162.964357 374.624564 SGB 6514.565578 -2848.696891 -2470.804948 1195.063739 TOTAL 6607.092096 -2729.563203 -2307.840591 1569.688303 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 410.706765 165579.597232 -12.376347 165977.927650 EL 2061.232529 -4521.817880 93.511284 -2367.074066 SGB -2470.804948 3115.025664 -106.285384 537.935332 TOTAL 1.134346 164172.805016 -25.150446 164148.788916 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5102.382364 NONPOLAR 10.802267 SGB TOT -898.578345 SOLV TOT -887.776078 TOTALE 163097.702070 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 92.526518 119.133689 162.964357 374.624564 SGB 6514.565578 -2848.696891 -2470.804948 1195.063739 TOTAL 6607.092096 -2729.563203 -2307.840591 1569.688303 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 410.706765 165579.597232 -12.376347 165977.927650 EL 2061.232529 -4521.817880 93.511284 -2367.074066 SGB -2470.804948 3115.025664 -106.285384 537.935332 TOTAL 1.134346 164172.805016 -25.150446 164148.788916 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5102.382364 NONPOLAR 10.802267 SGB TOT -898.578345 SOLV TOT -887.776078 TOTALE 163097.702070 Summary for structure: INITIAL ENERGY 163097.702 Global, backbone 0.855 Global, all heavy at 2.041 Local, N/CA/C/O 0.689 Local, all heavy ato 1.834 CLUSTERING PARAMETERS Number of data points: 48 Number of descriptors: 36 Number of clusters: 8 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 6 8 0.75 0.77 0.76 0.13 2 6 18 0.75 0.76 0.76 0.13 3 5 13 0.77 0.79 0.78 0.11 4 5 22 0.76 0.79 0.78 0.13 5 7 38 0.75 0.78 0.76 0.15 6 5 37 0.75 0.77 0.75 0.14 7 7 27 0.74 0.76 0.75 0.15 8 7 1 0.79 0.90 0.85 0.35 Data selected from clustering: 8 0.75 0.85 Big cluster found: 8 0.3539528141392591 Clusters added; will try again ... Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 6 8 0.75 0.77 0.76 0.13 2 6 18 0.75 0.76 0.76 0.13 3 5 13 0.77 0.79 0.78 0.11 4 5 22 0.76 0.79 0.78 0.13 5 7 38 0.75 0.78 0.76 0.15 6 5 37 0.75 0.77 0.75 0.14 7 7 27 0.74 0.76 0.75 0.15 8 3 1 0.85 0.90 0.85 0.25 9 1 46 0.79 0.79 0.79 0.00 10 3 45 0.79 0.79 0.79 0.09 Data selected from clustering: 10 0.75 0.85 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.76 1.76 0.77 1.62 Pass 1 163061.47 163013.94 -47.52 2.30 0.94 1.80 0.93 1.62 WARNING: sampling failure in side opt: 0.5324794542393647 (will revert to previous best ...) Pass 2 163013.94 163013.94 0.00 3.35 0.94 1.80 0.93 1.62 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 0.76 1.83 0.81 1.69 Pass 1 163077.63 163014.57 -63.05 1.99 0.95 1.72 0.94 1.54 Pass 2 163014.57 163014.36 -0.22 2.77 0.95 1.73 0.94 1.54 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 0.78 1.80 0.79 1.67 Pass 1 163067.37 163012.58 -54.79 1.92 0.95 1.71 0.94 1.54 Pass 2 163012.58 163012.81 0.22 2.82 0.95 1.72 0.94 1.54 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 0.78 1.88 0.83 1.74 Pass 1 163067.23 163013.54 -53.69 2.16 0.95 1.72 0.94 1.54 Pass 2 163013.54 163012.90 -0.64 2.77 0.95 1.73 0.94 1.54 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 0.76 1.63 0.79 1.55 Pass 1 163065.40 163013.11 -52.29 1.88 0.95 1.72 0.94 1.54 Pass 2 163013.11 163012.49 -0.62 3.41 0.95 1.73 0.94 1.55 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.75 1.60 0.78 1.52 Pass 1 163070.93 163015.39 -55.55 1.70 0.95 1.70 0.94 1.53 Pass 2 163015.39 163014.45 -0.93 3.44 0.95 1.72 0.94 1.54 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.75 1.58 0.76 1.51 Pass 1 163065.05 163014.64 -50.41 1.84 0.95 1.70 0.94 1.52 Pass 2 163014.64 163014.70 0.06 2.88 0.95 1.72 0.94 1.54 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 0.85 2.06 0.69 1.86 Pass 1 163090.04 163020.08 -69.96 2.72 0.94 1.80 0.93 1.62 Pass 2 163020.08 163020.58 0.50 2.79 0.94 1.81 0.93 1.63 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 0.79 2.01 0.67 1.85 Pass 1 163077.43 163019.48 -57.96 3.00 0.94 1.80 0.93 1.62 Pass 2 163019.48 163019.90 0.42 2.79 0.94 1.81 0.93 1.63 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 0.79 1.96 0.65 1.79 Pass 1 163082.55 163019.43 -63.13 2.64 0.94 1.80 0.93 1.62 Pass 2 163019.43 163019.92 0.49 2.77 0.94 1.81 0.93 1.63 Results so far: 5 38 163012.49288858780 0.95 1.73 0.94 1.55 3 13 163012.80586137160 0.95 1.72 0.94 1.54 4 22 163012.89812790810 0.95 1.73 0.94 1.54 1 8 163013.94481757390 0.94 1.80 0.93 1.62 2 18 163014.35621099010 0.95 1.73 0.94 1.54 6 37 163014.45496720320 0.95 1.72 0.94 1.54 7 27 163014.69581442920 0.95 1.72 0.94 1.54 9 46 163019.89704652540 0.94 1.81 0.93 1.63 10 45 163019.92115643530 0.94 1.81 0.93 1.63 8 1 163020.57910723400 0.94 1.81 0.93 1.63 Initial Minimized Side Opt Final ENERGY 163097.702 0.000 0.000163012.493 Global, ba 0.855 0.000 0.000 0.949 Global, al 2.041 0.000 0.000 1.729 Local, N/C 0.689 0.000 0.000 0.942 Local, all 1.834 0.000 0.000 1.545 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_27:OD1 [No apparent H-bonds] _:ASP_27:OD2 ============================================ Now working on new loop ... ============================================ _:ASP_41 _:GLY_46 6 Starting loop conformation: _:ASP_41 -60.32 -162.12 162.59 WARNING: above phi/psi not represented by library GENback Actual angles -60.32 -162.12 Closest rotamer -75.00 -175.00 Delta -14.68 -12.88 _:ASN_42 -100.00 20.00 171.18 _:GLY_43 -145.44 149.79 -180.00 WARNING: above phi/psi not represented by library GLYback Actual angles -145.44 149.79 Closest rotamer -150.00 155.00 Delta -4.56 5.21 _:VAL_44 -150.00 -175.00 -180.00 _:ASP_45 -60.00 -90.00 -180.00 WARNING: above phi/psi not represented by library GENback Actual angles -60.00 -90.00 Closest rotamer -80.00 -75.00 Delta -20.00 15.00 _:GLY_46 -170.00 -145.00 179.52 WARNING: above phi/psi not represented by library GLYback Actual angles -170.00 -145.00 Closest rotamer -165.00 -145.00 Delta 5.00 0.00 Parameters for generating loops ... Minimum conformations: 1 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 6 1.25 4.58 6 1.25 4.58 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.34 30 0.76 5.50 30 0.76 5.50 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.07 6 1.25 4.58 6 1.25 4.58 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.33 30 0.76 5.50 30 0.76 5.50 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 6 1.42 4.58 6 1.42 4.58 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.38 33 0.76 5.55 33 0.76 5.55 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 10 1.41 4.58 10 1.41 4.58 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.57 40 0.76 5.55 40 0.76 5.55 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.06 9 1.79 4.58 9 1.79 4.58 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 0.72 58 0.76 5.53 58 0.76 5.53 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.08 16 1.58 4.58 16 1.58 4.58 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.20 96 0.76 5.53 96 0.76 5.53 Number of closed loops found: 0 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.09 18 1.26 4.58 18 1.26 4.58 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.71 146 0.76 5.54 146 0.76 5.54 Number of closed loops found: 2 0.50 0.09 Results of loop screening 20.00 0.00 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 1 1.24 1.24 1.24 Loops rejected for phi/psi 1 1.98 1.98 1.98 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 0 N/A N/A N/A Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: Best loop that was rejected: 1.241068214423228 failed theta test: 156.1131588734824 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.09 29 1.42 4.58 29 1.42 4.58 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 1.85 197 0.76 5.55 197 0.76 5.55 Number of closed loops found: 0 0.50 0.10 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.11 50 1.45 4.76 50 1.45 4.76 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 3.35 349 0.76 5.66 349 0.76 5.66 Number of closed loops found: 12 0.50 0.10 Results of loop screening 20.00 0.02 Loops NOT rejected 5 1.33 1.64 2.32 Loops rejected for theta 5 1.28 1.94 2.74 Loops rejected for phi/psi 1 2.42 2.42 2.42 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 1 1.74 1.74 1.74 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 0 N/A N/A N/A Histogram of accepted loops: 1.0 2.0 4 2.0 3.0 1 Best loop that was rejected: 1.280460929406113 failed theta test: 90.43539613574995 failed phi/psi test: -16.21071789901504 90.53300894897838 failed back test failed side test: _:VAL_44 0.5999999999999998 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 79596.849509 701.423607 174.868756 80473.141872 SGB 6488.795808 -2834.955662 -2438.527188 1215.312958 TOTAL 86085.645316 -2133.532055 -2263.658432 81688.454829 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 353.667974 166733.002919 -12.530735 167074.140158 EL 2024.219629 -4402.860005 94.399195 -2284.241182 SGB -2438.527188 3043.830112 -105.071113 500.231811 TOTAL -60.639585 165373.973026 -23.202653 165290.130787 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5077.728380 NONPOLAR 8.602817 SGB TOT -923.656423 SOLV TOT -915.053606 TOTALE 244347.987243 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 79596.849509 701.423607 174.868756 80473.141872 SGB 6488.795808 -2834.955662 -2438.527188 1215.312958 TOTAL 86085.645316 -2133.532055 -2263.658432 81688.454829 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 353.667974 166733.002919 -12.530735 167074.140158 EL 2024.219629 -4402.860005 94.399195 -2284.241182 SGB -2438.527188 3043.830112 -105.071113 500.231811 TOTAL -60.639585 165373.973026 -23.202653 165290.130787 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -5077.728380 NONPOLAR 8.602817 SGB TOT -923.656423 SOLV TOT -915.053606 TOTALE 244347.987243 Summary for structure: INITIAL ENERGY 244347.987 Global, backbone 3.327 Global, all heavy at 3.969 Local, N/CA/C/O 3.084 Local, all heavy ato 3.894 Parameters for generating loops ... Minimum conformations: 64 Initial middle residue: _:GLY_43 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 Numerical loop closure. Side chains included as screen. Loop split: sample from both sides. Hydrogens with non-zero radii included. Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.12 50 1.45 4.76 50 1.45 4.76 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 3.35 349 0.76 5.66 349 0.76 5.66 Number of closed loops found: 12 0.50 0.10 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.14 71 1.16 4.72 71 1.16 4.72 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 7.95 1041 0.66 5.56 1041 0.66 5.56 Number of closed loops found: 77 0.40 0.13 Results of loop screening 20.00 0.11 Loops NOT rejected 23 1.28 1.93 2.81 Loops rejected for theta 33 1.06 1.70 2.46 Loops rejected for phi/psi 17 0.89 1.48 2.78 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 2 1.53 1.75 1.97 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 2 1.39 1.43 1.48 Histogram of accepted loops: 1.0 2.0 13 2.0 3.0 10 Best loop that was rejected: 0.8943901359135856 failed phi/psi test: 59.55240116353151 103.0758056434752 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ASP_41 _:GLY_43 0.24 188 1.10 4.66 188 1.10 4.66 Right branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:GLY_46 _:GLY_43 17.06 3211 0.71 5.55 3211 0.71 5.55 Number of closed loops found: 484 0.30 0.22 Results of loop screening 20.00 0.64 Loops NOT rejected 135 0.87 1.67 2.50 Loops rejected for theta 211 0.89 1.70 2.79 Loops rejected for phi/psi 128 0.86 1.66 2.44 Loops rejected for omega1 0 N/A N/A N/A Loops rejected for omega2 0 N/A N/A N/A Loops rejected for C-beta 6 1.44 1.89 2.50 Loops rejected for L/R 3 1.10 1.32 1.50 Loops rejected for sidechn 1 1.68 1.68 1.68 Histogram of accepted loops: 0.0 1.0 3 1.0 2.0 117 2.0 3.0 15 Best loop that was rejected: 0.8567862127155511 failed phi/psi test: 15.91421273905739 32.75366982918381 failed back test failed side test: _:VAL_44 0.5999999999999998 CLUSTERING PARAMETERS Number of data points: 135 Number of descriptors: 60 Number of clusters: 12 Number of clusters allowed to increase. Maximum tries in each cluster: 5 Number of iterations: 1 Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 11 105 0.87 1.35 0.87 4.47 2 31 35 1.19 1.83 1.34 3.53 3 26 29 1.44 1.77 1.52 2.51 4 18 51 1.67 2.11 1.92 3.33 5 5 47 1.70 2.03 1.96 4.09 6 4 81 1.73 2.08 2.07 3.16 7 3 74 1.52 1.60 1.59 2.81 8 17 116 1.49 1.93 1.58 2.51 9 2 79 1.74 1.79 1.79 0.85 10 8 87 1.55 2.09 1.98 2.02 11 2 1 1.94 1.96 1.96 0.17 12 8 26 1.61 2.50 2.19 3.45 Data selected from clustering: 12 0.87 2.19 Big cluster found: 12 3.452346636181157 Clusters added; will try again ... Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 7 105 0.87 1.30 0.87 4.24 2 24 36 1.07 1.82 1.25 3.26 3 25 29 1.44 1.76 1.52 2.40 4 18 51 1.67 2.11 1.92 3.33 5 5 48 1.73 2.08 2.01 3.07 6 2 81 2.03 2.07 2.07 0.81 7 3 74 1.52 1.60 1.59 2.81 8 17 116 1.49 1.93 1.58 2.51 9 2 79 1.74 1.79 1.79 0.85 10 8 87 1.55 2.09 1.98 2.02 11 2 1 1.94 1.96 1.96 0.17 12 10 34 1.61 2.04 1.72 2.32 13 6 75 0.93 1.72 1.61 3.93 14 6 3 2.12 2.50 2.40 2.98 Data selected from clustering: 14 0.87 2.40 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.87 1.89 0.55 1.62 Pass 15725472.28 162699.38********** 3.49 1.23 2.07 0.63 1.55 Pass 2 162699.38 162692.41 -6.97 4.47 1.26 1.90 0.65 1.34 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 1.25 2.07 0.88 1.81 Pass 1 163869.32 162691.58 -1177.74 4.91 1.09 1.72 0.62 1.26 WARNING: sampling failure in side opt: 0.5596205651236232 (will revert to previous best ...) Pass 2 162691.58 162691.58 0.00 4.36 1.09 1.72 0.62 1.26 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 1.52 3.06 1.34 2.89 Pass 1 162855.80 162717.23 -138.56 3.54 1.45 2.84 1.30 2.55 Pass 2 162717.23 162716.96 -0.27 4.44 1.45 2.84 1.30 2.55 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 1.92 3.14 1.91 2.94 Pass 1 162854.16 162720.14 -134.03 2.81 1.73 2.78 1.78 2.76 Pass 2 162720.14 162714.85 -5.29 5.84 1.62 2.73 1.69 2.77 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 2.01 2.99 1.56 2.62 Pass 1 162873.67 162724.08 -149.59 3.31 2.03 2.73 1.71 2.81 Pass 2 162724.08 162723.93 -0.15 3.55 2.03 2.73 1.71 2.81 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 2.07 2.97 1.78 2.77 Pass 1 162848.96 162721.11 -127.85 2.99 1.85 2.66 1.53 2.54 Pass 2 162721.11 162714.59 -6.51 4.47 1.87 2.71 1.56 2.60 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 1.59 3.01 1.43 2.78 Pass 1 162893.20 162739.47 -153.73 4.21 2.08 2.98 1.53 2.65 Pass 2 162739.47 162739.62 0.15 4.07 2.08 2.98 1.53 2.65 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 1.58 3.06 1.73 3.05 Pass 1 162835.93 162720.27 -115.66 6.31 1.73 2.78 1.78 2.76 Pass 2 162720.27 162715.64 -4.63 5.92 1.62 2.73 1.69 2.77 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 1.79 3.06 1.63 3.33 Pass 1 162882.68 162748.81 -133.87 4.60 1.89 2.80 1.60 2.61 Pass 2 162748.81 162746.69 -2.12 4.64 1.89 2.80 1.61 2.61 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 1.98 3.29 1.77 3.05 Pass 1 162907.58 162728.77 -178.81 4.15 1.60 2.80 1.39 2.64 Pass 2 162728.77 162727.02 -1.75 4.48 1.60 2.73 1.40 2.57 =================== Working on cluster 11 Summary of side chain addition/minim: Initial 1.96 2.96 1.53 2.68 Pass 1 162958.51 162738.60 -219.91 5.32 2.04 2.99 1.52 2.68 Pass 2 162738.60 162738.45 -0.15 4.88 2.05 3.00 1.52 2.68 =================== Working on cluster 12 Summary of side chain addition/minim: Initial 1.72 2.89 1.37 2.53 WARNING: Serious failure in tn minimization dE = 1.195168759615626 Will revert to starting coordinates ... Pass 1 162858.24 162711.02 -147.23 5.37 1.44 2.54 1.15 2.23 WARNING: sampling failure in side opt: 1.357767662295373 (will revert to previous best ...) Pass 2 162711.02 162711.02 0.00 5.29 1.44 2.54 1.15 2.23 =================== Working on cluster 13 Summary of side chain addition/minim: Initial 1.61 2.14 1.41 1.95 Pass 1 162882.28 162720.92 -161.36 3.38 1.56 1.87 1.36 1.41 Pass 2 162720.92 162720.72 -0.21 3.83 1.56 1.87 1.36 1.41 =================== Working on cluster 14 Summary of side chain addition/minim: Initial 2.40 2.86 1.47 2.37 Pass 1 162846.71 162706.46 -140.26 2.80 2.11 2.39 1.34 1.76 Pass 2 162706.46 162706.19 -0.26 3.84 2.11 2.39 1.34 1.76 Results so far: 2 36 162691.57532043230 1.09 1.72 0.62 1.26 1 105 162692.40783479820 1.26 1.90 0.65 1.34 14 3 162706.19265592060 2.11 2.39 1.34 1.76 12 34 162711.01814803090 1.44 2.54 1.15 2.23 6 81 162714.59398243680 1.87 2.71 1.56 2.60 4 51 162714.84836978580 1.62 2.73 1.69 2.77 8 116 162715.64019301260 1.62 2.73 1.69 2.77 3 29 162716.95965214010 1.45 2.84 1.30 2.55 13 75 162720.71749592670 1.56 1.87 1.36 1.41 5 48 162723.92620035720 2.03 2.73 1.71 2.81 10 87 162727.01881922300 1.60 2.73 1.40 2.57 11 1 162738.44745676350 2.05 3.00 1.52 2.68 7 74 162739.61738507120 2.08 2.98 1.53 2.65 9 79 162746.69010227730 1.89 2.80 1.61 2.61 Initial Minimized Side Opt Final ENERGY 244347.987 0.000 0.000162691.575 Global, ba 3.327 0.000 0.000 1.090 Global, al 3.969 0.000 0.000 1.719 Local, N/C 3.084 0.000 0.000 0.623 Local, all 3.894 0.000 0.000 1.261 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_41:OD1 [No apparent H-bonds] _:ASP_41:OD2 [No apparent H-bonds] _:ASN_42:OD1 INTRA HBOND (side/main) _:ASN_42:ND2 _:TYR_38:O 1 2.775 [No apparent H-bonds] _:ASP_45:OD1 [No apparent H-bonds] _:ASP_45:OD2 Summary of side chain addition/minim: Initial 2.31 2.48 1.07 1.30 WARNING: excessive rounding errors in line search Pass 1 162750.79 -3028.62-165779.41 44.64 1.12 1.83 0.73 1.47 Pass 2 -3028.62 -3062.39 -33.76 44.09 0.27 1.09 0.35 1.09 Results so far: (HELIX) 6 27 -3062.39 0.27 1.09 0.35 1.09 4 1 -3050.38 0.26 0.96 0.32 0.95 5 19 -3045.53 0.28 1.04 0.27 1.02 3 11 -3030.96 0.28 0.92 0.35 0.91 1 44 -3030.44 0.60 1.38 0.51 1.33 2 28 -3017.60 0.58 1.23 0.50 1.20 Initial Minimized Side Opt Final ENERGY -2877.573 -3038.781 -3040.344 -3062.388 Global, ba 0.000 0.230 0.245 0.272 Global, al 0.000 0.381 0.753 1.093 Local, N/C 0.000 0.242 0.257 0.348 Local, all 0.000 0.373 0.746 1.095 H-bond contacts in current structure: [No apparent H-bonds] _:ASP_27:OD1 [No apparent H-bonds] _:ASP_27:OD2 [No apparent H-bonds] _:GLU_29:OE1 [No apparent H-bonds] _:GLU_29:OE2 [No apparent H-bonds] _:THR_30:OG1 [No apparent H-bonds] _:GLU_32:OE1 [No apparent H-bonds] _:GLU_32:OE2 [No apparent H-bonds] _:LYS_33:NZ INTRA HBOND (side/side) _:LYS_36:NZ _:TRP_48:NE1 1 3.049 [No apparent H-bonds] _:GLN_37:OE1 [No apparent H-bonds] _:GLN_37:NE2 [No apparent H-bonds] _:TYR_38:OH [No apparent H-bonds] _:ASN_40:OD1 INTRA HBOND (side/main) _:ASN_40:ND2 _:LYS_36:O 1 2.764 [No apparent H-bonds] _:ASP_41:OD1 [No apparent H-bonds] _:ASP_41:OD2 [No apparent H-bonds] _:ASN_42:OD1 INTRA HBOND (side/main) _:ASN_42:ND2 _:TYR_38:O 1 2.771 [No apparent H-bonds] _:ASP_45:OD1 [No apparent H-bonds] _:ASP_45:OD2 TOTAL TIME ELAPSED: plop_job 2350.989947451279