This is PLOP, version 1-4m What path for the control file? Contents of the control file: load pdb 2igd.pdb loop predict _:42 _: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 0.180 cross 0.000 child 0.010 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 0.20 Assign coordinates 0.03 Initialize symmetry 0.00 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 are the parameters chosen for loop predict: LOOP GENERATION PARAMETERS Overlap factor: 0.7000000000000000 Minimum conformations: 32 Residues per stage: 30 Base resolution for backbone: 5.000000000000000 Resolution for side chains: 10.00000000000000 No dihedral restrictions. No Cartesian restrictions. Standard bonds/angles imposed. If sampling failure, will revert to original structure. SIDE CHAIN PARAMETERS Distance cutoffs for non-loop SCs: 0.000000000000000 Non-loop SCs included in steric screening. [PARAMETERS FOR 1st ITERATION OF SC OPT] SC SCREENING PARAMETERS Initial overlap factor: 0.7500000000000000 Minimum overlap factor: 0.7000000000000000 Total iterations: 1 SCs NOT randomized prior to optimization. New tree-based energy routines used. If sampling failure, will revert to original structure. SGB and LR NEVER updated. MINIMIZATION PARAMETERS Desired final RMS gradient: 1.0000000000000000E-002 Maximum number of iterations to achieve self-consistency: 2 Maximum number of TN iterations: 65 Iterations between NBlist/LR updates: 2 LR forces will be updated less frequently than SR. NB list will be updated during minim. SGB will be updated during minim. Born alpha will NOT be updated during minim [PARAMETERS FOR 2nd ITERATION OF SC OPT] SC SCREENING PARAMETERS Initial overlap factor: 0.7500000000000000 Minimum overlap factor: 0.7000000000000000 Total iterations: 1 SCs NOT randomized prior to optimization. New tree-based energy routines used. If sampling failure, will revert to original structure. SGB and LR updated after each cycle. MINIMIZATION PARAMETERS Desired final RMS gradient: 1.0000000000000000E-003 Maximum number of iterations to achieve self-consistency: 3 Maximum number of TN iterations: 65 Iterations between NBlist/LR updates: 2 LR forces will be updated less frequently than SR. NB list will be updated during minim. SGB will be updated during minim. Born alpha will NOT be updated during minim I/O PARAMETERS Scored loop conformations written to: ./plop_job.loop.pdb Energies and RMSDs written to: ./plop_job.loop.rmsd CLUSTERING PARAMETERS Number of clusters: 20 Number of clusters allowed to increase. Maximum tries in each cluster: 10 Number of iterations: 2 Energy cutoff for re-clustering: 15.00000000000000 Rotamer type assignments: 1 _:ASN_42 BACK 1 GENback SIDE 1 ASNside OMEGA is trans 2 _:GLY_43 BACK 1 GLYback OMEGA is trans 3 _:VAL_44 BACK 1 GENback SIDE 1 VALside OMEGA is trans 4 _:ASP_45 BACK 1 GENback SIDE 1 ASPside OMEGA is trans 5 _:GLY_46 BACK 1 GLYback OMEGA is trans ============================================ Now working on new loop ... ============================================ _:ASN_42 _:GLY_46 5 Starting loop conformation: _:ASN_42 -104.15 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 Minimum overlap factors for free atoms: (only those with ofac < 1 shown) _: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 * Stem distance: 11.72063313136283 H-bond contacts in current structure: [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 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 Parameters for generating loops ... Minimum conformations: 32 Initial middle residue: _:VAL_44 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 _:ASN_42 _:VAL_44 0.08 15 1.47 2.95 15 1.47 2.95 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.07 13 1.42 2.95 13 1.42 2.95 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.08 15 1.72 2.95 15 1.72 2.95 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.08 22 1.67 2.95 22 1.67 2.95 Right branch (res,ofac,nstage): 120.00 60.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.10 12 0.70 2.97 12 0.70 2.97 Right branch (res,ofac,nstage): 110.00 55.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.11 12 0.65 2.97 12 0.65 2.97 Right branch (res,ofac,nstage): 100.00 50.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.12 15 0.66 2.97 15 0.66 2.97 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.15 23 0.62 2.97 23 0.62 2.97 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.08 22 1.67 2.95 22 1.67 2.95 Right branch (res,ofac,nstage): 90.00 45.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.15 23 0.62 2.97 23 0.62 2.97 Number of closed loops found: 2 0.50 0.08 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.09 28 1.23 2.95 28 1.23 2.95 Right branch (res,ofac,nstage): 80.00 40.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.17 31 0.68 3.27 31 0.68 3.27 Number of closed loops found: 3 0.50 0.09 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.09 32 1.33 2.95 32 1.33 2.95 Right branch (res,ofac,nstage): 70.00 35.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.21 35 0.76 2.97 35 0.76 2.97 Number of closed loops found: 4 0.50 0.09 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.11 47 1.16 2.95 47 1.16 2.95 Right branch (res,ofac,nstage): 60.00 30.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.20 30 0.56 2.97 30 0.56 2.97 Number of closed loops found: 5 0.50 0.09 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.13 66 1.23 2.95 66 1.23 2.95 Right branch (res,ofac,nstage): 50.00 25.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.22 58 0.59 2.97 58 0.59 2.97 Number of closed loops found: 11 0.50 0.09 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.18 141 0.59 2.95 141 0.59 2.95 Right branch (res,ofac,nstage): 40.00 20.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.37 117 0.62 3.27 117 0.62 3.27 Number of closed loops found: 67 0.40 0.10 Results of loop screening 25.00 0.07 Loops NOT rejected 8 0.49 1.33 1.49 Loops rejected for theta 44 0.71 1.37 1.88 Loops rejected for phi/psi 12 1.17 1.42 2.01 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 1.08 1.28 1.48 Loops rejected for L/R 0 N/A N/A N/A Loops rejected for sidechn 1 1.86 1.86 1.86 Histogram of accepted loops: 0.0 1.0 1 1.0 2.0 7 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.26 257 0.26 2.95 257 0.26 2.95 Right branch (res,ofac,nstage): 30.00 15.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 0.51 204 0.48 2.99 204 0.48 2.99 Number of closed loops found: 259 0.30 0.10 Results of loop screening 25.00 0.28 Loops NOT rejected 28 0.33 0.99 1.47 Loops rejected for theta 139 0.43 1.32 1.84 Loops rejected for phi/psi 50 0.64 1.35 1.90 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 32 0.45 1.31 1.53 Loops rejected for L/R 1 1.48 1.48 1.48 Loops rejected for sidechn 9 0.41 1.14 1.59 Histogram of accepted loops: 0.0 1.0 13 1.0 2.0 15 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:ASN_42 _:VAL_44 0.58 849 0.34 3.00 849 0.34 3.00 Right branch (res,ofac,nstage): 20.00 10.00 0.700 1 Stage: 1 _:GLY_46 _:VAL_44 1.00 572 0.56 3.14 572 0.56 3.14 Number of closed loops found: 1252 0.20 0.13 Results of loop screening 25.00 1.40 Loops NOT rejected 166 0.37 1.16 1.70 Loops rejected for theta 668 0.49 1.28 2.06 Loops rejected for phi/psi 251 0.45 1.29 2.04 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 92 0.67 1.37 1.84 Loops rejected for L/R 5 1.29 1.45 1.58 Loops rejected for sidechn 70 0.54 1.08 1.85 Histogram of accepted loops: 0.0 1.0 49 1.0 2.0 117 Side chains to be optimized on body of protein: ... distance cutoff = 0.000000000000000 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 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 Summary for structure: INITIAL ENERGY -2877.573 Global, backbone 0.000 Global, all heavy at 0.000 Local, N/CA/C/O 0.000 Local, all heavy ato 0.000 ------------------------------------------- Energy minimizing starting loop ... ------------------------------------------- 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 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 95.020327 110.976370 143.048507 349.045204 SGB 6321.061597 -2782.335253 -2395.154987 1143.571358 TOTAL 6416.081924 -2671.358882 -2252.106480 1492.616562 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 368.672990 -386.618779 -12.462929 -30.408718 EL 2050.809579 -4517.759647 103.105225 -2363.844842 SGB -2395.154987 3038.211508 -115.976708 527.079814 TOTAL 24.327582 -1866.166917 -25.334411 -1867.173746 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4950.667784 NONPOLAR 24.315217 SGB TOT -884.861627 SOLV TOT -860.546410 TOTALE -2905.754766 Summary for structure: MINIMIZED ENERGY -2905.755 Global, backbone 0.170 Global, all heavy at 0.361 Local, N/CA/C/O 0.205 Local, all heavy ato 0.380 Summary of side chain addition/minim: Initial 0.00 0.00 0.00 0.00 Pass 1 -2877.56 -2905.71 -28.14 2.11 0.17 0.36 0.21 0.38 Pass 2 -2905.71 -2905.81 -0.11 3.12 0.17 0.36 0.21 0.38 Summary for structure: SIDE OPT ENERGY -2905.812 Global, backbone 0.170 Global, all heavy at 0.362 Local, N/CA/C/O 0.206 Local, all heavy ato 0.381 CLUSTERING PARAMETERS Number of data points: 166 Number of descriptors: 48 Number of clusters: 20 Number of clusters allowed to increase. Maximum tries in each cluster: 10 Number of iterations: 2 Energy cutoff for re-clustering: 15.00000000000000 Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 3 124 1.21 1.28 1.28 1.58 2 7 88 1.27 1.33 1.28 0.57 3 9 16 1.26 1.38 1.35 0.69 4 8 9 1.30 1.40 1.31 0.60 5 8 108 1.22 1.36 1.34 0.92 6 6 135 1.30 1.38 1.37 0.71 7 8 84 0.37 0.57 0.40 0.77 8 5 33 0.46 0.74 0.49 1.43 9 6 26 0.44 0.64 0.50 0.97 10 7 104 1.18 1.38 1.20 1.35 11 10 37 1.35 1.43 1.41 0.66 12 7 19 0.60 0.74 0.61 0.67 13 8 63 1.16 1.27 1.21 1.61 14 10 118 1.21 1.50 1.26 1.14 15 10 164 1.37 1.48 1.44 1.83 16 28 60 0.68 1.27 0.83 1.75 17 10 76 1.31 1.51 1.51 0.75 18 5 143 1.28 1.50 1.28 1.49 19 4 150 1.56 1.67 1.62 0.88 20 7 153 1.58 1.70 1.66 0.71 Data selected from clustering: 20 0.40 1.66 Big cluster found: 20 0.7121378007574299 Big cluster found: 15 1.828419143795374 Clusters added; will try again ... Summary of cluster results; time = 0.010 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 3 124 1.21 1.28 1.28 1.58 2 7 88 1.27 1.33 1.28 0.57 3 9 16 1.26 1.38 1.35 0.69 4 8 9 1.30 1.40 1.31 0.60 5 8 108 1.22 1.36 1.34 0.92 6 6 135 1.30 1.38 1.37 0.71 7 8 84 0.37 0.57 0.40 0.77 8 5 33 0.46 0.74 0.49 1.43 9 6 26 0.44 0.64 0.50 0.97 10 7 104 1.18 1.38 1.20 1.35 11 10 37 1.35 1.43 1.41 0.66 12 7 19 0.60 0.74 0.61 0.67 13 8 63 1.16 1.27 1.21 1.61 14 10 118 1.21 1.50 1.26 1.14 15 4 162 1.44 1.48 1.47 0.76 16 28 60 0.68 1.27 0.83 1.75 17 10 76 1.31 1.51 1.51 0.75 18 5 143 1.28 1.50 1.28 1.49 19 4 150 1.56 1.67 1.62 0.88 20 2 156 1.58 1.59 1.59 0.16 21 3 149 1.66 1.70 1.70 0.38 22 2 151 1.68 1.69 1.68 0.25 23 2 166 1.37 1.38 1.38 2.09 24 4 163 1.40 1.47 1.43 0.25 Data selected from clustering: 24 0.40 1.70 WARNING: cluster_drive ntry maxed out =================== Working on cluster 1 Summary of side chain addition/minim: Initial 1.28 3.03 1.36 2.45 Pass 1 4164.53 -2875.38 -7039.92 2.50 1.30 2.88 1.19 2.37 Pass 2 -2875.38 -2875.23 0.16 2.96 1.30 2.88 1.19 2.37 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 1.28 2.75 1.32 2.62 Pass 1 2369.72 -2872.89 -5242.61 4.02 1.28 2.58 0.92 2.07 Pass 2 -2872.89 -2872.95 -0.06 3.09 1.28 2.58 0.92 2.07 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 1.35 2.75 1.40 2.88 Pass 1 -606.51 -2872.88 -2266.37 3.90 1.28 2.58 0.92 2.07 Pass 2 -2872.88 -2872.80 0.08 3.10 1.28 2.58 0.92 2.07 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 1.31 2.74 1.41 2.86 Pass 1 2689.84 -2872.87 -5562.71 3.56 1.28 2.58 0.92 2.07 Pass 2 -2872.87 -2872.80 0.07 3.18 1.28 2.58 0.92 2.07 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 1.34 3.05 1.36 2.64 Pass 1 -2738.19 -2877.01 -138.81 3.41 1.23 2.70 1.04 2.19 Pass 2 -2877.01 -2877.02 -0.02 3.00 1.23 2.70 1.04 2.19 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 1.37 2.73 1.40 2.57 Pass 1 4323.31 -2870.82 -7194.13 3.88 1.30 2.95 1.13 2.43 Pass 2 -2870.82 -2870.83 -0.01 3.07 1.30 2.95 1.13 2.42 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.40 1.09 0.29 0.88 Pass 1 -2063.37 -2905.21 -841.84 2.26 0.17 0.36 0.21 0.38 Pass 2 -2905.21 -2905.18 0.03 3.11 0.17 0.36 0.21 0.38 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 0.49 1.28 0.66 1.25 Pass 1 2648.12 -2905.84 -5553.96 2.74 0.17 0.36 0.21 0.38 Pass 2 -2905.84 -2905.76 0.08 3.13 0.17 0.36 0.21 0.38 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 0.50 1.26 0.63 1.01 Pass 1 -646.85 -2900.05 -2253.20 2.28 0.34 0.84 0.30 0.75 Pass 2 -2900.05 -2900.04 0.01 3.11 0.34 0.84 0.30 0.75 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 1.20 2.72 1.29 2.47 Pass 1 -1801.70 -2876.26 -1074.56 3.62 1.25 2.78 1.07 2.26 Pass 2 -2876.26 -2876.24 0.02 2.92 1.25 2.78 1.07 2.26 =================== Working on cluster 11 Summary of side chain addition/minim: Initial 1.41 2.59 1.44 2.67 Pass 1 -2425.50 -2870.03 -444.52 2.77 1.47 2.61 1.45 2.61 Pass 2 -2870.03 -2874.25 -4.22 4.00 1.47 2.65 1.46 2.73 =================== Working on cluster 12 Summary of side chain addition/minim: Initial 0.61 1.11 0.45 1.02 Pass 1 -1966.82 -2904.85 -938.04 2.27 0.17 0.36 0.20 0.38 Pass 2 -2904.85 -2905.23 -0.38 3.13 0.17 0.36 0.20 0.38 =================== Working on cluster 13 Summary of side chain addition/minim: Initial 1.21 2.86 1.24 2.44 Pass 1 -2584.50 -2876.79 -292.29 2.71 1.23 2.70 1.04 2.19 Pass 2 -2876.79 -2876.77 0.02 2.99 1.23 2.70 1.04 2.19 =================== Working on cluster 14 Summary of side chain addition/minim: Initial 1.26 2.83 1.26 2.21 Pass 1 -2699.59 -2875.51 -175.91 2.19 1.30 2.88 1.19 2.37 Pass 2 -2875.51 -2875.56 -0.05 2.96 1.30 2.88 1.19 2.37 =================== Working on cluster 15 Summary of side chain addition/minim: Initial 1.47 2.81 1.69 2.77 Pass 1 -2733.33 -2880.78 -147.45 2.54 1.63 2.94 1.78 2.75 Pass 2 -2880.78 -2880.87 -0.09 3.11 1.63 2.94 1.78 2.75 =================== Working on cluster 16 Summary of side chain addition/minim: Initial 0.83 1.94 0.77 1.62 Pass 1 -1856.51 -2886.71 -1030.21 2.40 0.85 2.12 0.79 1.69 Pass 2 -2886.71 -2886.79 -0.08 3.16 0.85 2.12 0.79 1.69 =================== Working on cluster 17 Summary of side chain addition/minim: Initial 1.51 2.68 1.48 2.60 Pass 1 -2298.07 -2869.41 -571.34 2.37 1.47 2.61 1.45 2.61 Pass 2 -2869.41 -2875.29 -5.88 4.02 1.48 2.65 1.46 2.73 =================== Working on cluster 18 Summary of side chain addition/minim: Initial 1.28 2.68 1.63 2.62 Pass 1 -2746.48 -2863.47 -116.99 2.60 1.57 3.04 1.79 2.84 Pass 2 -2863.47 -2870.30 -6.83 4.13 1.61 3.07 1.76 2.83 =================== Working on cluster 19 Summary of side chain addition/minim: Initial 1.62 3.13 1.62 2.93 Pass 1 -2720.98 -2874.67 -153.69 2.07 1.56 2.85 1.50 2.67 Pass 2 -2874.67 -2875.86 -1.19 3.14 1.56 2.85 1.50 2.67 =================== Working on cluster 20 Summary of side chain addition/minim: Initial 1.59 3.01 1.59 2.95 Pass 1 -2641.39 -2876.20 -234.81 3.03 1.55 2.82 1.55 2.61 WARNING: Serious failure in tn minimization dE = 1.022614420218815 Will revert to starting coordinates ... WARNING: Minimization may not be converged. Pass 2 -2876.20 -2877.52 -1.32 3.72 1.55 2.81 1.55 2.60 =================== Working on cluster 21 Summary of side chain addition/minim: Initial 1.70 3.11 1.79 3.01 Pass 1 -2715.72 -2876.55 -160.83 2.46 1.59 2.81 1.67 2.59 Pass 2 -2876.55 -2878.60 -2.06 4.59 1.53 2.81 1.51 2.62 =================== Working on cluster 22 Summary of side chain addition/minim: Initial 1.68 3.11 1.68 2.95 Pass 1 -2717.93 -2878.38 -160.45 2.29 1.53 2.81 1.51 2.62 Pass 2 -2878.38 -2877.97 0.41 3.04 1.54 2.81 1.51 2.62 =================== Working on cluster 23 Summary of side chain addition/minim: Initial 1.38 2.47 1.37 2.80 Pass 1 -1597.76 -2868.29 -1270.54 2.24 1.36 2.61 1.39 2.81 Pass 2 -2868.29 -2868.38 -0.09 3.15 1.36 2.61 1.39 2.80 =================== Working on cluster 24 Summary of side chain addition/minim: Initial 1.43 2.84 1.68 2.81 Pass 1 -2391.75 -2880.77 -489.02 2.45 1.63 2.93 1.78 2.75 Pass 2 -2880.77 -2880.78 0.00 3.15 1.63 2.94 1.78 2.75 Results so far: 8 33 -2905.76 0.17 0.36 0.21 0.38 12 19 -2905.23 0.17 0.36 0.20 0.38 7 84 -2905.18 0.17 0.36 0.21 0.38 9 26 -2900.04 0.34 0.84 0.30 0.75 16 60 -2886.79 0.85 2.12 0.79 1.69 15 162 -2880.87 1.63 2.94 1.78 2.75 24 163 -2880.78 1.63 2.94 1.78 2.75 21 149 -2878.60 1.53 2.81 1.51 2.62 22 151 -2877.97 1.54 2.81 1.51 2.62 20 156 -2877.52 1.55 2.81 1.55 2.60 5 108 -2877.02 1.23 2.70 1.04 2.19 13 63 -2876.77 1.23 2.70 1.04 2.19 10 104 -2876.24 1.25 2.78 1.07 2.26 19 150 -2875.86 1.56 2.85 1.50 2.67 14 118 -2875.56 1.30 2.88 1.19 2.37 17 76 -2875.29 1.48 2.65 1.46 2.73 1 124 -2875.23 1.30 2.88 1.19 2.37 11 37 -2874.25 1.47 2.65 1.46 2.73 2 88 -2872.95 1.28 2.58 0.92 2.07 4 9 -2872.80 1.28 2.58 0.92 2.07 3 16 -2872.80 1.28 2.58 0.92 2.07 6 135 -2870.83 1.30 2.95 1.13 2.42 18 143 -2870.30 1.61 3.07 1.76 2.83 23 166 -2868.38 1.36 2.61 1.39 2.80 Number of candidates retained for next round: 22 Summary of cluster results; time = 0.000 (cluster#,#data,repr.,rmsd min/max/rep,rms) 1 1 18 0.37 0.37 0.37 0.00 2 1 16 0.42 0.42 0.42 0.00 3 1 19 0.44 0.44 0.44 0.00 4 2 8 0.44 0.46 0.44 0.24 5 1 17 0.43 0.43 0.43 0.00 6 1 15 0.47 0.47 0.47 0.00 7 1 7 0.53 0.53 0.53 0.00 8 1 5 0.60 0.60 0.60 0.00 9 1 12 0.54 0.54 0.54 0.00 10 1 3 0.62 0.62 0.62 0.00 11 1 6 0.62 0.62 0.62 0.00 12 1 1 0.64 0.64 0.64 0.00 13 1 2 0.63 0.63 0.63 0.00 14 2 20 0.56 0.57 0.56 0.56 15 1 4 0.74 0.74 0.74 0.00 16 1 11 0.47 0.47 0.47 0.00 17 1 10 0.46 0.46 0.46 0.00 18 1 9 0.50 0.50 0.50 0.00 19 1 14 0.64 0.64 0.64 0.00 20 1 22 0.74 0.74 0.74 0.00 Data selected from clustering: 20 0.37 0.74 =================== Working on cluster 1 Summary of side chain addition/minim: Initial 0.37 1.15 0.31 0.86 Pass 1 -2716.61 -2900.61 -184.00 2.25 0.34 0.84 0.30 0.75 Pass 2 -2900.61 -2900.56 0.05 3.13 0.34 0.84 0.30 0.75 =================== Working on cluster 2 Summary of side chain addition/minim: Initial 0.42 1.13 0.28 0.88 Pass 1 -1398.71 -2905.26 -1506.55 2.21 0.17 0.36 0.20 0.38 Pass 2 -2905.26 -2905.23 0.03 3.19 0.17 0.36 0.21 0.38 =================== Working on cluster 3 Summary of side chain addition/minim: Initial 0.44 1.62 0.44 1.33 Pass 1 -2646.62 -2900.58 -253.96 2.32 0.34 0.84 0.30 0.75 Pass 2 -2900.58 -2900.49 0.08 3.16 0.34 0.84 0.30 0.75 =================== Working on cluster 4 Summary of side chain addition/minim: Initial 0.44 1.20 0.54 1.11 Pass 1 -1787.17 -2900.08 -1112.91 2.25 0.34 0.84 0.30 0.75 Pass 2 -2900.08 -2900.07 0.01 3.12 0.34 0.84 0.30 0.75 =================== Working on cluster 5 Summary of side chain addition/minim: Initial 0.43 1.10 0.32 0.89 Pass 1 715.45 -2905.19 -3620.65 2.31 0.17 0.36 0.21 0.38 Pass 2 -2905.19 -2905.25 -0.05 3.17 0.17 0.36 0.21 0.38 =================== Working on cluster 6 Summary of side chain addition/minim: Initial 0.47 1.20 0.37 0.92 Pass 1 775.89 -2905.07 -3680.96 2.24 0.17 0.36 0.20 0.38 Pass 2 -2905.07 -2905.25 -0.18 3.18 0.17 0.36 0.21 0.38 =================== Working on cluster 7 Summary of side chain addition/minim: Initial 0.53 1.67 0.62 1.49 Pass 1 11842.28 -2900.03 -14742.31 2.25 0.34 0.84 0.30 0.75 Pass 2 -2900.03 -2899.97 0.05 3.17 0.34 0.84 0.30 0.75 =================== Working on cluster 8 Summary of side chain addition/minim: Initial 0.60 1.17 0.49 1.03 Pass 1 -2741.54 -2900.14 -158.60 2.25 0.34 0.84 0.30 0.75 Pass 2 -2900.14 -2899.91 0.22 3.14 0.34 0.84 0.30 0.75 =================== Working on cluster 9 Summary of side chain addition/minim: Initial 0.54 1.65 0.71 1.46 Pass 1 -1174.78 -2900.11 -1725.33 2.38 0.34 0.84 0.30 0.75 Pass 2 -2900.11 -2899.99 0.11 3.18 0.34 0.84 0.30 0.75 =================== Working on cluster 10 Summary of side chain addition/minim: Initial 0.62 1.15 0.51 1.03 Pass 1 -2038.93 -2905.89 -866.95 2.47 0.17 0.36 0.21 0.38 Pass 2 -2905.89 -2905.80 0.09 3.18 0.17 0.36 0.21 0.38 =================== Working on cluster 11 Summary of side chain addition/minim: Initial 0.62 1.19 0.53 1.10 Pass 1 -2766.49 -2905.21 -138.72 2.39 0.17 0.36 0.21 0.38 Pass 2 -2905.21 -2905.30 -0.09 3.16 0.17 0.36 0.21 0.38 =================== Working on cluster 12 Summary of side chain addition/minim: Initial 0.64 1.16 0.56 1.08 Pass 1 6165.04 -2905.90 -9070.94 2.25 0.17 0.36 0.21 0.38 Pass 2 -2905.90 -2905.82 0.08 3.18 0.17 0.36 0.21 0.38 =================== Working on cluster 13 Summary of side chain addition/minim: Initial 0.63 1.12 0.50 1.07 Pass 1 10122.57 -2905.60 -13028.17 2.20 0.17 0.36 0.21 0.38 Pass 2 -2905.60 -2905.88 -0.28 3.18 0.17 0.36 0.21 0.38 =================== Working on cluster 14 Summary of side chain addition/minim: Initial 0.56 1.20 0.46 0.92 Pass 1 -780.92 -2905.23 -2124.30 2.32 0.17 0.36 0.20 0.38 Pass 2 -2905.23 -2905.26 -0.03 3.17 0.17 0.36 0.21 0.38 =================== Working on cluster 15 Summary of side chain addition/minim: Initial 0.74 1.41 0.69 1.18 Pass 1 15026.30 -2899.91 -17926.20 2.38 0.34 0.84 0.30 0.75 Pass 2 -2899.91 -2899.98 -0.07 3.16 0.34 0.84 0.30 0.75 =================== Working on cluster 16 Summary of side chain addition/minim: Initial 0.47 1.28 0.54 1.27 Pass 1 269522.53 -2906.01-272428.54 2.57 0.17 0.36 0.21 0.38 Pass 2 -2906.01 -2905.77 0.23 3.19 0.17 0.36 0.21 0.38 =================== Working on cluster 17 Summary of side chain addition/minim: Initial 0.46 1.26 0.55 1.24 Pass 1 53917.44 -2905.77 -56823.21 2.43 0.17 0.36 0.21 0.38 Pass 2 -2905.77 -2905.77 0.00 3.18 0.17 0.36 0.21 0.38 =================== Working on cluster 18 Summary of side chain addition/minim: Initial 0.50 1.29 0.55 1.24 Pass 1 109770.32 -2905.86-112676.17 2.61 0.17 0.36 0.21 0.38 Pass 2 -2905.86 -2905.85 0.00 3.18 0.17 0.36 0.21 0.38 =================== Working on cluster 19 Summary of side chain addition/minim: Initial 0.64 1.50 1.03 1.33 Pass 1 -1776.83 -2890.30 -1113.47 3.14 0.33 1.10 0.28 1.04 Pass 2 -2890.30 -2900.13 -9.83 4.01 0.34 0.84 0.30 0.75 =================== Working on cluster 20 Summary of side chain addition/minim: Initial 0.74 1.69 1.21 1.57 Pass 1********** -2881.35********** 2.32 0.68 1.12 1.07 1.01 Pass 2 -2881.35 -2881.20 0.14 3.04 0.68 1.12 1.07 1.01 Results so far: 37 13 -2905.88 0.17 0.36 0.21 0.38 42 28 -2905.85 0.17 0.36 0.21 0.38 36 12 -2905.82 0.17 0.36 0.21 0.38 34 18 -2905.80 0.17 0.36 0.21 0.38 40 30 -2905.77 0.17 0.36 0.21 0.38 41 29 -2905.77 0.17 0.36 0.21 0.38 8 33 -2905.76 0.17 0.36 0.21 0.38 35 24 -2905.30 0.17 0.36 0.21 0.38 38 138 -2905.26 0.17 0.36 0.21 0.38 30 82 -2905.25 0.17 0.36 0.21 0.38 29 85 -2905.25 0.17 0.36 0.21 0.38 12 19 -2905.23 0.17 0.36 0.20 0.38 26 83 -2905.23 0.17 0.36 0.21 0.38 7 84 -2905.18 0.17 0.36 0.21 0.38 25 91 -2900.56 0.34 0.84 0.30 0.75 27 92 -2900.49 0.34 0.84 0.30 0.75 43 34 -2900.13 0.34 0.84 0.30 0.75 28 27 -2900.07 0.34 0.84 0.30 0.75 9 26 -2900.04 0.34 0.84 0.30 0.75 33 31 -2899.99 0.34 0.84 0.30 0.75 39 20 -2899.98 0.34 0.84 0.30 0.75 31 25 -2899.97 0.34 0.84 0.30 0.75 32 23 -2899.91 0.34 0.84 0.30 0.75 16 60 -2886.79 0.85 2.12 0.79 1.69 44 140 -2881.20 0.68 1.12 1.07 1.01 15 162 -2880.87 1.63 2.94 1.78 2.75 24 163 -2880.78 1.63 2.94 1.78 2.75 21 149 -2878.60 1.53 2.81 1.51 2.62 22 151 -2877.97 1.54 2.81 1.51 2.62 20 156 -2877.52 1.55 2.81 1.55 2.60 5 108 -2877.02 1.23 2.70 1.04 2.19 13 63 -2876.77 1.23 2.70 1.04 2.19 10 104 -2876.24 1.25 2.78 1.07 2.26 19 150 -2875.86 1.56 2.85 1.50 2.67 14 118 -2875.56 1.30 2.88 1.19 2.37 17 76 -2875.29 1.48 2.65 1.46 2.73 1 124 -2875.23 1.30 2.88 1.19 2.37 11 37 -2874.25 1.47 2.65 1.46 2.73 2 88 -2872.95 1.28 2.58 0.92 2.07 4 9 -2872.80 1.28 2.58 0.92 2.07 3 16 -2872.80 1.28 2.58 0.92 2.07 6 135 -2870.83 1.30 2.95 1.13 2.42 18 143 -2870.30 1.61 3.07 1.76 2.83 23 166 -2868.38 1.36 2.61 1.39 2.80 Initial Minimized Side Opt Final ENERGY -2877.573 -2905.755 -2905.812 -2905.884 Global, ba 0.000 0.170 0.170 0.170 Global, al 0.000 0.361 0.362 0.362 Local, N/C 0.000 0.205 0.206 0.206 Local, all 0.000 0.380 0.381 0.381 H-bond contacts in current structure: [No apparent H-bonds] _:ASN_42:OD1 INTRA HBOND (side/main) _:ASN_42:ND2 _:TYR_38:O 1 2.751 [No apparent H-bonds] _:ASP_45:OD1 [No apparent H-bonds] _:ASP_45:OD2 TOTAL TIME ELAPSED: plop_job 279.8299937453121