This is PLOP, version 1-4t What path for the control file? Contents of the control file: homolog load 2igd_1hz5.align 1hz5.pdb chain A native 2igd.pdb tail aligned ssgaps yes g2x yes conserve yes initfile 2igd_homo.init gapfile 2igd_homo.gap insertfile 2igd_homo.insert sidefile 2igd_homo.side finalfile 2igd_homo.rmsd structure write 2igd_homo.pdb Here are the parameters chosen for homology model building: BASIC MODEL BUILDING OPTIONS Number of templates: 1 Template: 1 Alignment: 2igd_1hz5.align PDB file: 1hz5.pdb Chain: A Model: 1 Number of HET groups to be included: 0 Minimum overlap factor: 0.7500000000000000 Maximum angle deviations: 25.00000000000000 Gaps allowed within secondary structure. Problematic X->P substitutions repaired. Problematic G->X substitutions repaired. Aligned portion of N-terminal tail retained; rest discarded Aligned portion of C-terminal tail retained; rest discarded I/O PARAMETERS Initial model (chain breaks) written to: 2igd_homo.init Structure after gap closure written to: 2igd_homo.gap Structure after templates break fixes: ./multi.pdb Structure after insertions written to: 2igd_homo.insert Final completed structures written to: 2igd_homo.rmsd MINIMIZATION PARAMETERS Desired final RMS gradient: 0.1000000000000000 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 NOW READING IN THE TEMPLATE STRUCTURE ... 1hz5.pdb Chain: A Model: 1 This is X-RAY DATA Temperature information detected: 100.0000000000000 pH information detected. pH = 6.000000000000000 Based on pH, will substitute HIP for HIS. Ions being ignored ...ZN Ions being ignored ...ZN Ions being ignored ...ZN Ions being ignored ...ZN Ions being ignored ...ZN Ions being ignored ...ZN Ions being ignored ...ZN Ions being ignored ...ZN Ions being ignored ...ZN Ions being ignored ...ZN Waters being ignored ... Timings for various book-keeping steps: build 0.220 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 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 72 (charged) 17 (polar) 25 (glycine) 5 (hydrophobic) 25 Number of atoms 1128 [sparse atoms] 97 Number of bonds 1142 Number of angles 2033 Number of torsions 3229 Number of 1/4s 2926 Number of waters 0 Number of ions 0 Number of HET 0 Partial charges and molecular weights: Protein chain A -3.0 8036.9 Entire system -3.0 8036.9 Time for dynamic memory allocation: 0.000000000000000 Time for secondary sructure initialization: 0.000000000000000 Residue numbers & secondary structure in template ... 1 E 11 3 0 2 V 12 4 -2 3 T 13 5 -2 4 I 14 6 -2 5 K 15 7 -1 6 A 16 8 -1 7 N 17 9 -1 8 L 18 10 -1 9 I 19 11 -1 10 F 20 12 0 11 A 21 13 0 12 N 22 14 0 13 G 23 15 0 14 S 24 16 0 15 T 25 17 -2 16 Q 26 18 -2 17 T 27 19 -2 18 A 28 20 -2 19 E 29 21 -2 20 F 30 22 -2 21 K 31 23 -2 22 G 32 24 -2 23 T 33 25 0 24 F 34 26 4 25 E 35 27 4 26 . -9999 -9999 0 27 K 36 28 4 28 A 37 29 4 29 T 38 30 4 30 S 39 31 4 31 E 40 32 4 32 A 41 33 4 33 Y 42 34 4 34 A 43 35 4 35 Y 44 36 4 36 A 45 37 4 37 D 46 38 4 38 T 47 39 4 39 L 48 40 4 40 K 49 41 4 41 K 50 42 4 42 D 51 43 4 43 N 52 44 4 44 G 53 45 0 45 E 54 46 0 46 W 55 47 -2 47 T 56 48 -2 48 V 57 49 -2 49 D 58 50 -2 50 V 59 51 -2 51 A 60 52 -2 52 D 61 53 3 53 K 62 54 3 54 G 63 55 3 55 Y 64 56 0 56 T 65 57 -1 57 L 66 58 -1 58 N 67 59 -1 59 I 68 60 -1 60 K 69 61 -1 61 F 70 62 -2 WARNING: the alignment contains gaps within secondary structure elements ... 25 E 4 27 K 4 Will continue with these gaps anyways ... WARNING: there are worrisome substitutions in the middle of a helix ... 40 KG 14 Total number of residues: 57 Number of identical residues: 8 Timings for various book-keeping steps: build 0.170 cross 0.000 child 0.000 iper 0.000 rev 0.000 info 0.010 resat 0.000 rank 0.000 covpt 0.000 sparse 0.000 Time for assigning nb parameters: 0.000000000000000 Number of chains 1 Number of residues 57 (charged) 16 (polar) 20 (glycine) 4 (hydrophobic) 17 Number of atoms 888 [sparse atoms] 72 Number of bonds 894 Number of angles 1600 Number of torsions 2515 Number of 1/4s 2323 Number of waters 0 Number of ions 0 Number of HET 0 Partial charges and molecular weights: Protein chain A -2.0 6247.9 Entire system -2.0 6247.9 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 894 675 203 16 0 0.01 ANGL 1600 972 612 0 16 0.02 TORS 2515 1377 1106 0 32 0.04 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 20547.432705 481.739915 169.478117 21198.650737 SGB 6249.625490 -2760.646297 -2323.924269 1165.054924 TOTAL 26797.058195 -2278.906382 -2154.446152 22363.705661 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ *************** *************** -12.253580 *************** EL 6524.801027 -3887.957260 50.254896 2687.098662 SGB -2323.924269 2564.734473 -63.052419 177.757785 TOTAL *************** *************** -25.051103 *************** TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4879.883865 NONPOLAR 30.613487 SGB TOT -1213.146887 SOLV TOT -1182.533400 TOTALE *************** WARNING: large bond energies found: 201 199 _:THR_12:C 201 _:LEU_13:N 1845.71 397 395 _:GLU_25:C 397 _:THR_26:N 618.83 627 623 _:VAL_40:C 625 _:ASP_41:N 18059.96 WARNING: large angl energies found: #,atoms,energy,angle,eq; 2nd line:types 367 _:THR_12:O _:THR_12:C _:LEU_13:N 26.5 89.9 122.9 O C N N C O 369 _:THR_12:C _:LEU_13:N _:LEU_13:CA 18.2 156.5 121.9 C N CT1 C N CT1 373 _:LEU_13:H _:LEU_13:N _:LEU_13:CA 13.9 83.7 118.4 H N CT1 CT1 N H 720 _:GLU_25:CA _:GLU_25:C _:THR_26:N 147.4 33.5 116.6 CT1 C N CT1 C N 721 _:GLU_25:O _:GLU_25:C _:THR_26:N 23.5 154.0 122.9 O C N N C O 723 _:GLU_25:C _:THR_26:N _:THR_26:CA 111.6 36.3 121.9 C N CT1 C N CT1 727 _:THR_26:H _:THR_26:N _:THR_26:CA 16.4 156.1 118.4 H N CT1 CT1 N H 1128 _:VAL_40:CA _:VAL_40:C _:ASP_41:N 25.2 82.2 116.6 CT1 C N CT1 C N 1129 _:VAL_40:O _:VAL_40:C _:ASP_41:N 33.3 85.9 122.9 O C N N C O WARNING: large tor energies found: 542 _:THR_12:CA _:LEU_13:N _:THR_12:C _:THR_12:O 12.72 1732 _:VAL_40:CA _:ASP_41:N _:VAL_40:C _:VAL_40:O 15.11 WARNING: large 14 energies found: 1042 _:GLU_25:N _:THR_26:N ********** 4480.22 -19.72 1043 _:GLU_25:HA _:THR_26:N 5.02 -2.38 2.17 1044 _:GLU_25:CB _:THR_26:N 8.18 4.06 -4.54 1046 _:GLU_25:CA _:THR_26:CA ********** 93.23 -1.47 1048 _:GLU_25:O _:THR_26:CA 6.20 -4.82 5.79 1050 _:GLU_25:C _:THR_26:CB ********** 45.86 -9.00 1051 _:GLU_25:C _:THR_26:C 59.31 17.80 -17.63 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: 0.30 Time for contact parameter loading: 0.01 Time for sgb parameter loading: 0.01 Time for dynamic memory allocation: 0.00 Time for covalent parameter assignment: 0.12 Time for nobonded list initialization: 0.02 Time for covalent list initialization: 0.00 Time for sgb initialization: 1.44 Number of native atoms loaded: 29 Number of excluded atoms: 0 Current RMSDs: Aligned res, calpha/ 56 5.50 Aligned res, calpha/ 168 5.73 Aligned res, calpha/ 446 6.09 All res, calpha/calp 57 5.50 All res, calpha/back 171 5.73 All res, calpha/heav 457 6.09 Here are the gaps in alignment: 1 _:THR_12 _:LEU_13 2 _:VAL_40 _:ASP_41 Here are the insertions in alignment: 1 _:ALA_24 _:THR_26 Here are template transitions in alignment: ============================================= Now attempting to build close gaps ... ============================================= ---------------------------------------------- Attempting to close gap: _:THR_12 _:LEU_13 Closure criterion for _:THR_12 _:LEU_13 5.61 3.94 WARNING: this loop cannot close: _:THR_12 _:LEU_13 Attempting to expand closure region ... N-side: 0 0 T C-side: 0 -2 T SUCCEEDED: _:LYS_11 _:LEU_13 Closure criterion for _:LYS_11 _:LEU_13 7.31 7.36 Reconstructing gap region: _:LYS_11 _:LEU_13 Dihedral/Cartesian distances to target: _:LYS_11 144.29 0.00 _:THR_12 123.73 0.00 _:LEU_13 160.99 0.00 Side chains to be checked: 1 _:GLU_57 2 _:ASN_9 3 _:THR_56 4 _:ILE_8 5 _:LYS_14 6 _:LYS_11 7 _:THR_12 8 _:LEU_13 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 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 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.04 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:LYS_11 _:LEU_13 0.05 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! Attempting to expand closure region ... N-side: 0 0 T C-side: 0 -2 T SUCCEEDED: _:GLY_10 _:LEU_13 Closure criterion for _:GLY_10 _:LEU_13 5.36 10.82 Reconstructing gap region: _:GLY_10 _:LEU_13 Dihedral/Cartesian distances to target: _:GLY_10 169.46 0.00 _:LYS_11 144.29 0.00 _:THR_12 123.73 0.00 _:LEU_13 160.99 0.00 Side chains to be checked: 1 _:ASN_38 2 _:ILE_8 3 _:GLU_57 4 _:LYS_14 5 _:ASN_9 6 _:THR_56 7 _:LYS_11 8 _:THR_12 9 _:LEU_13 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:GLY_10 _:LEU_13 0.13 1 0.00 0.00 1 0.00 0.00 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:GLY_10 _:LEU_13 0.12 1 0.00 0.00 1 0.00 0.00 Number of closed loops found: 1 0.50 0.09 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 Results of loop screening 25.00 0.00 Loops NOT rejected 1 0.00 0.00 0.00 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 18713.962485 426.538194 140.456393 19280.957071 SGB 6256.316228 -2770.483736 -2320.669548 1165.162944 TOTAL 24970.278712 -2343.945542 -2180.213156 20446.120014 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ *************** *************** -12.636471 *************** EL 6520.293987 -3835.677212 42.206919 2726.823695 SGB -2320.669548 1443.557001 -55.397375 -932.509922 TOTAL *************** *************** -25.826927 *************** TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4879.883865 NONPOLAR 30.613487 SGB TOT -2326.561296 SOLV TOT -2295.947809 TOTALE *************** WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 Summary for structure: INITIAL ENERGY ********** Global, backbone 0.000 Global, all heavy at 0.000 Local, N/CA/C/O 0.000 Local, all heavy ato 0.000 Now picking the loop nearest to original one: ... number of possibilities = 1 Best one: 1 2.624121137264996 Problems have been detected for _:LEU_13 The side chain does not have enough room to fit! ofac_min = 0.70 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 18713.962485 426.538194 140.456393 19280.957071 SGB 6256.316228 -2770.483736 -2320.669548 1165.162944 TOTAL 24970.278712 -2343.945542 -2180.213156 20446.120014 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ *************** *************** -12.850940 *************** EL 6520.293987 -3835.677212 46.565820 2731.182596 SGB -2320.669548 1443.557001 -59.916608 -937.029156 TOTAL *************** *************** -26.201729 *************** TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4879.883865 NONPOLAR 30.613487 SGB TOT -2331.080529 SOLV TOT -2300.467042 TOTALE *************** Final loop conformation: _:GLY_10 -180.00 165.00 -180.00 _:LYS_11 60.00 -120.00 -180.00 _:THR_12 -115.00 10.00 176.82 _:LEU_13 -159.36 -148.46 -171.29 Dihedral/Cartesian distances to target: _:GLY_10 165.00 0.00 _:LYS_11 60.00 0.00 _:THR_12 65.00 0.00 _:LEU_13 31.54 0.00 ---------------------------------------------- Attempting to close gap: _:VAL_40 _:ASP_41 Closure criterion for _:VAL_40 _:ASP_41 8.12 3.94 WARNING: this loop cannot close: _:VAL_40 _:ASP_41 Attempting to expand closure region ... N-side: 0 4 T C-side: 0 0 T SUCCEEDED: _:VAL_40 _:GLY_42 Closure criterion for _:VAL_40 _:GLY_42 10.56 7.36 WARNING: this loop cannot close: _:VAL_40 _:GLY_42 Attempting to expand closure region ... N-side: 0 4 T C-side: 0 -2 T SUCCEEDED: _:GLY_39 _:GLY_42 Closure criterion for _:GLY_39 _:GLY_42 7.01 10.82 Reconstructing gap region: _:GLY_39 _:GLY_42 Dihedral/Cartesian distances to target: _:GLY_39 141.35 0.00 _:VAL_40 126.82 0.00 _:ASP_41 115.55 20.24 _:GLY_42 158.24 0.00 Side chains to be checked: 1 _:ASP_37 2 _:ASN_36 3 _:ASN_38 4 _:GLU_57 5 _:VAL_43 6 _:LEU_6 7 _:ILE_8 8 _:LYS_32 9 _:VAL_55 10 _:PHE_53 11 _:TRP_44 12 _:THR_56 13 _:VAL_40 14 _:ASP_41 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:GLY_39 _:GLY_42 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:GLY_39 _:GLY_42 0.11 1 21.62 21.62 1 21.62 21.62 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:GLY_39 _:GLY_42 0.10 1 21.62 21.62 1 21.62 21.62 Number of closed loops found: 1 0.50 0.09 Results of loop screening 25.00 0.00 Loops NOT rejected 1 15.54 15.54 15.54 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: 10.0 11.0 1 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 653.693640 379.256798 117.347317 1150.297755 SGB 6273.794570 -2795.755889 -2338.326782 1139.711899 TOTAL 6927.488210 -2416.499092 -2220.979465 2290.009654 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ *************** *************** 54578.456338 *************** EL 6542.486568 -3890.868349 78.205140 2729.823359 SGB -2338.326782 1128.950243 -104.195825 -1313.572364 TOTAL *************** *************** 54552.465653 *************** TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4879.883865 NONPOLAR 30.613487 SGB TOT -2715.417549 SOLV TOT -2684.804062 TOTALE *************** Summary for structure: INITIAL ENERGY ********** Global, backbone 15.538 Global, all heavy at 17.515 Local, N/CA/C/O 0.146 Local, all heavy ato 2.412 Now picking the loop nearest to original one: ... number of possibilities = 1 Best one: 1 3.849823206040181 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 653.693640 379.256798 117.347317 1150.297755 SGB 6273.794570 -2795.755889 -2338.326782 1139.711899 TOTAL 6927.488210 -2416.499092 -2220.979465 2290.009654 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ *************** *************** 54578.187213 *************** EL 6542.486568 -3890.868349 68.691663 2720.309882 SGB -2338.326782 1128.950243 -94.944360 -1304.320899 TOTAL *************** *************** 54551.934516 *************** TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4879.883865 NONPOLAR 30.613487 SGB TOT -2706.166084 SOLV TOT -2675.552597 TOTALE *************** Final loop conformation: _:GLY_39 150.00 -175.00 -180.00 _:VAL_40 -125.00 175.00 -180.00 _:ASP_41 40.00 55.00 176.30 _:GLY_42 -99.78 165.45 -171.71 Dihedral/Cartesian distances to target: _:GLY_39 150.00 0.00 _:VAL_40 175.00 0.00 _:ASP_41 95.54 0.11 _:GLY_42 165.45 0.00 Current RMSDs: Aligned res, calpha/ 56 5.35 Aligned res, calpha/ 168 5.55 Aligned res, calpha/ 446 6.15 All res, calpha/calp 57 5.35 All res, calpha/back 171 5.55 All res, calpha/heav 457 6.15 ============================================= Now attempting to build build insertions ... ============================================= ---------------------------------------------- Attempting to close gap: _:ALA_24 _:THR_26 Closure criterion for _:ALA_24 _:THR_26 3.80 7.36 Reconstructing gap region: _:ALA_24 _:THR_26 Dihedral/Cartesian distances to target: _:ALA_24 134.26 0.00 _:THR_26 139.00 0.00 Side chains to be checked: 1 _:VAL_22 2 _:LYS_29 3 _:ASP_23 4 _:GLU_28 5 _:THR_19 6 _:GLU_25 7 _:THR_26 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.09 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.14 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.65 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 5.08 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 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 40.00 20.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.07 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 30.00 15.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.08 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 20.00 10.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.13 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 10.00 5.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 0.55 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 5.00 5.00 0.750 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ALA_24 _:THR_26 3.98 0 0.00 0.00 0 0.00 0.00 WARNING: sampres/ofac both bottomed out! Attempting to expand closure region ... N-side: 1 5 T C-side: 1 4 T SUCCEEDED: _:ASP_23 _:THR_26 Closure criterion for _:ASP_23 _:THR_26 5.71 10.82 Reconstructing gap region: _:ASP_23 _:THR_26 Dihedral/Cartesian distances to target: _:ASP_23 136.04 0.00 _:ALA_24 134.26 0.00 _:THR_26 139.00 0.00 Removed from screening list: _:THR_50 Side chains to be checked: 1 _:VAL_22 2 _:THR_2 3 _:TYR_4 4 _:GLU_28 5 _:TYR_46 6 _:LYS_29 7 _:THR_19 8 _:ASP_23 9 _:GLU_25 10 _:THR_26 Left branch (res,ofac,nstage): 120.00 60.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 110.00 55.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 100.00 50.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.05 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 90.00 45.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.06 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 80.00 40.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 70.00 35.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.10 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 60.00 30.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.12 0 0.00 0.00 0 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.19 3 0.00 0.00 3 0.00 0.00 Left branch (res,ofac,nstage): 50.00 25.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.20 3 0.00 0.00 3 0.00 0.00 Number of closed loops found: 3 0.50 0.08 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 Results of loop screening 25.00 0.01 Loops NOT rejected 0 N/A N/A N/A Loops rejected for theta 2 0.00 0.00 0.00 Loops rejected for phi/psi 1 0.00 0.00 0.00 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: 0.000000000000000 failed theta test: 147.4268112289001 Left branch (res,ofac,nstage): 40.00 20.00 0.700 1 WARNING: At least 3 atoms needed for alignment 0 Stage: 1 _:ASP_23 _:THR_26 0.29 4 0.00 0.00 4 0.00 0.00 Number of closed loops found: 4 0.40 0.09 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 Results of loop screening 25.00 0.01 Loops NOT rejected 2 0.00 0.00 0.00 Loops rejected for theta 2 0.00 0.00 0.00 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 2 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 50.270088 109.071367 120.212101 279.553556 SGB 6275.366236 -2801.550698 -2329.033517 1144.782021 TOTAL 6325.636323 -2692.479331 -2208.821416 1424.335576 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 469.254514 *************** -12.588655 *************** EL 1933.023070 -3741.529921 74.508321 -1733.998530 SGB -2329.033517 1085.609113 -87.012010 -1330.436414 TOTAL 73.244067 *************** -25.092343 *************** TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4879.883865 NONPOLAR 30.613487 SGB TOT -2736.504742 SOLV TOT -2705.891255 TOTALE *************** WARNING: At least 3 atoms needed for alignment 0 WARNING: At least 3 atoms needed for alignment 0 Summary for structure: INITIAL ENERGY ********** Global, backbone 0.000 Global, all heavy at 0.000 Local, N/CA/C/O 0.000 Local, all heavy ato 0.000 Now picking the loop nearest to original one: ... number of possibilities = 2 Best one: 2 1.426523510530369 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 38.955856 81.813800 116.990104 237.759761 SGB 6275.444069 -2800.602543 -2332.616508 1142.225017 TOTAL 6314.399925 -2718.788743 -2215.626404 1379.984778 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 469.362032 *************** -12.831327 *************** EL 1938.855667 -3766.073013 89.050553 -1738.166793 SGB -2332.616508 1101.516768 -101.118950 -1332.218691 TOTAL 75.601190 *************** -24.899725 *************** TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4879.883865 NONPOLAR 30.613487 SGB TOT -2737.261031 SOLV TOT -2706.647544 TOTALE *************** Final loop conformation: _:ASP_23 -105.00 40.00 -180.00 _:ALA_24 -165.00 105.00 -180.00 _:GLU_25 75.00 5.00 173.46 _:THR_26 -118.51 -93.05 -173.09 Dihedral/Cartesian distances to target: _:ASP_23 75.00 0.00 _:ALA_24 105.00 0.00 _:GLU_25 75.00 0.00 _:THR_26 86.95 0.00 Current RMSDs: Aligned res, calpha/ 56 5.35 Aligned res, calpha/ 168 5.55 Aligned res, calpha/ 446 6.15 All res, calpha/calp 57 5.35 All res, calpha/back 171 5.55 All res, calpha/heav 457 6.15 Here are the gaps that have been closed: 1 _:THR_12 _:LEU_13 _:GLY_10 _:LEU_13 0.00 SUCCESS 2 _:VAL_40 _:ASP_41 _:GLY_39 _:GLY_42 7.15 SUCCESS Here are the template transitions that have been closed: Here are the insertions that have been built: 1 _:ALA_24 _:THR_26 _:ASP_23 _:THR_26 0.00 SUCCESS Here are the x2p segments that have been built: Here are the g2x segments that have been built: Here is the status of the loops: 1 _:GLY_10 _:LEU_13 0.00 2 _:VAL_22 _:VAL_22 0.00 3 _:VAL_40 _:GLY_42 7.15 4 _:LYS_51 _:LYS_51 0.00 Dihedral/C-alpha errors in loops: 1 _:GLY_10 _:LEU_13 _:GLY_10 165.00 0.00 _:LYS_11 60.00 0.00 _:THR_12 65.00 0.00 _:LEU_13 31.54 0.00 2 _:VAL_22 _:VAL_22 _:VAL_22 163.68 0.00 3 _:VAL_40 _:GLY_42 _:VAL_40 175.00 0.00 _:ASP_41 95.54 7.15 _:GLY_42 165.45 0.00 4 _:LYS_51 _:LYS_51 _:LYS_51 171.60 0.00 Here are portions of the structure that have gotten worse during building ... ============================================= Now optimizing side chains ... ============================================= Problems have been detected for _:LEU_13 The side chain does not have enough room to fit! ofac_min = 0.70 WARNING: above phi/psi not represented by library GENback Actual angles 150.00 -153.97 Closest rotamer -175.00 -180.00 Delta 35.00 -26.03 Problems have been detected for _:ALA_21 The phi/psi angles do not correspond to allowed region of Ramachandran plot (as defined by the rotamer library) phi: 150.00 psi: -153.97 Problems have been detected for _:ALA_49 There are steric clashes with other backbone atoms ... _:ALA_49:O _:THR_50:CB 0.73 1 Problems have been detected for _:THR_50 There are steric clashes with other backbone atoms ... _:THR_50:CB _:ALA_49:O 0.73 1 WARNING: above phi/psi not represented by library GENback Actual angles 101.01 -8.57 Closest rotamer 75.00 5.00 Delta -26.01 13.57 The phi/psi angles do not correspond to allowed region of Ramachandran plot (as defined by the rotamer library) phi: 101.01 psi: -8.57 The side chain does not have enough room to fit! ofac_min = 0.70 A more stringent (and time consuming) test comes from adding side chains to the complete structure. To do so, use command *side pred*. ------------------------------------------ NOW PRE-SCREENING ROTAMER STATES ... (res, # after screen, # total, ofac, rmsd_min, rmsd_max, time) _:VAL_1 17 17 0.00 -1.00 -1.00 0.00 _:THR_2 28 28 0.00 49.97 51.34 0.00 _:TYR_4 151 151 0.00 -1.00 -1.00 0.00 _:LEU_6 171 171 0.00 -1.00 -1.00 0.01 _:VAL_7 17 17 0.00 -1.00 -1.00 0.00 _:ILE_8 178 178 0.00 -1.00 -1.00 0.00 _:ASN_9 309 309 0.00 -1.00 -1.00 0.00 _:LYS_11 2091 2091 0.00 -1.00 -1.00 0.04 _:THR_12 28 28 0.00 -1.00 -1.00 0.00 _:LEU_13 171 171 0.00 -1.00 -1.00 0.00 _:LYS_14 2091 2091 0.00 -1.00 -1.00 0.05 _:GLU_16 958 958 0.00 -1.00 -1.00 0.01 _:THR_17 28 28 0.00 -1.00 -1.00 0.00 _:THR_18 28 28 0.00 -1.00 -1.00 0.00 _:THR_19 28 28 0.00 -1.00 -1.00 0.00 _:VAL_22 17 17 0.00 -1.00 -1.00 0.00 _:ASP_23 233 233 0.00 -1.00 -1.00 0.00 _:GLU_25 958 958 0.00 -1.00 -1.00 0.01 _:THR_26 28 28 0.00 -1.00 -1.00 0.01 _:GLU_28 958 958 0.00 -1.00 -1.00 0.01 _:LYS_29 2091 2091 0.00 -1.00 -1.00 0.05 _:PHE_31 141 141 0.00 -1.00 -1.00 0.01 _:LYS_32 2091 2091 0.00 -1.00 -1.00 0.04 _:GLN_33 877 877 0.00 -1.00 -1.00 0.01 _:ASN_36 309 309 0.00 -1.00 -1.00 0.00 _:ASP_37 233 233 0.00 -1.00 -1.00 0.00 _:ASN_38 309 309 0.00 -1.00 -1.00 0.00 _:VAL_40 17 17 0.00 -1.00 -1.00 0.00 _:ASP_41 233 233 0.00 22.48 25.82 0.00 _:VAL_43 17 17 0.00 -1.00 -1.00 0.00 _:TRP_44 168 168 0.00 -1.00 -1.00 0.00 _:THR_45 28 28 0.00 -1.00 -1.00 0.00 _:TYR_46 151 151 0.00 -1.00 -1.00 0.00 _:ASP_47 233 233 0.00 -1.00 -1.00 0.00 _:THR_50 28 28 0.00 -1.00 -1.00 0.00 _:LYS_51 2091 2091 0.00 -1.00 -1.00 0.04 _:PHE_53 141 141 0.00 -1.00 -1.00 0.01 _:THR_54 28 28 0.00 22.45 23.91 0.00 _:VAL_55 17 17 0.00 -1.00 -1.00 0.00 _:THR_56 28 28 0.00 11.59 12.95 0.00 _:GLU_57 958 958 0.00 -1.00 -1.00 0.01 ------------------------------------------ NOW PICKING ROTAMER STATE BY ENERGY ... (res, # rotamers, # evaluated, ofac, cluster, rot #, old rot #, times) _:VAL_1 17 10 0.75 1 26988 -1 0.01 **** _:THR_2 64 252 0.75 1 26334 -1 0.03 **** _:TYR_4 187 72 0.65 1 26728 -1 0.01 **** _:LEU_6 171 9 0.30 1 15920 -1 0.02 **** _:VAL_7 17 1 0.65 1 26994 -1 0.00 **** _:ILE_8 178 13 0.70 1 15612 -1 0.02 **** _:ASN_9 309 230 0.75 1 8627 -1 0.09 **** _:LYS_11 2103 9564 0.75 1 21176 -1 1.06 **** _:THR_12 64 648 0.75 1 26340 -1 0.03 **** _:LEU_13 171 3 0.70 1 15980 -1 0.00 **** _:LYS_14 2103 5932 0.75 1 19900 -1 0.73 **** _:GLU_16 958 409 0.75 1 12481 -1 0.21 **** _:THR_17 64 432 0.75 1 26331 -1 0.06 **** _:THR_18 64 432 0.75 1 26340 -1 0.05 **** _:THR_19 64 324 0.75 1 26339 -1 0.06 **** _:VAL_22 17 1 0.55 1 27003 -1 0.00 **** _:ASP_23 233 72 0.75 1 9517 -1 0.03 **** _:GLU_25 958 156 0.75 1 12904 -1 0.07 **** _:THR_26 64 72 0.70 1 26338 -1 0.01 **** _:GLU_28 958 319 0.75 1 12496 -1 0.21 **** _:LYS_29 2103 5669 0.75 1 17048 -1 0.71 **** _:PHE_31 141 3 0.45 1 26183 -1 0.01 **** _:LYS_32 2103 298 0.75 1 24108 -1 0.05 **** _:GLN_33 877 350 0.75 1 10567 -1 0.18 **** _:ASN_36 309 205 0.75 1 8773 -1 0.06 **** _:ASP_37 233 134 0.75 1 9379 -1 0.03 **** _:ASN_38 309 193 0.75 1 8793 -1 0.08 **** _:VAL_40 17 5 0.75 1 26994 -1 0.00 **** _:ASP_41 233 123 0.75 1 9405 -1 0.02 **** _:VAL_43 17 4 0.75 1 26990 -1 0.00 **** _:TRP_44 168 14 0.60 1 26636 -1 0.02 **** _:THR_45 64 72 0.75 1 26334 -1 0.01 **** _:TYR_46 187 972 0.75 1 26902 -1 0.06 **** _:ASP_47 233 103 0.75 1 9283 -1 0.03 **** _:THR_50 64 36 0.70 1 26332 -1 0.01 **** _:LYS_51 2103 7267 0.75 1 21176 -1 1.03 **** _:PHE_53 141 3 0.50 1 25961 -1 0.01 **** _:THR_54 64 216 0.75 1 26331 -1 0.03 **** _:VAL_55 17 1 0.70 1 26997 -1 0.00 **** _:THR_56 64 612 0.75 1 26331 -1 0.07 **** _:GLU_57 958 563 0.75 1 13729 -1 0.32 **** Time for iteration: 6.309999858960509 Rotamer placement not converged; flips: 41 ------------------------------------------ NOW PICKING ROTAMER STATE BY ENERGY ... (res, # rotamers, # evaluated, ofac, cluster, rot #, old rot #, times) _:VAL_1 17 10 0.75 1 26988 26988 0.00 _:THR_2 64 216 0.75 1 26334 26334 0.02 _:TYR_4 187 72 0.75 1 26776 26728 0.01 **** _:LEU_6 171 2 0.70 1 15918 15920 0.00 **** _:VAL_7 17 6 0.75 1 26988 26994 0.01 **** _:ILE_8 178 8 0.70 1 15604 15612 0.01 **** _:ASN_9 309 110 0.75 1 8625 8627 0.04 **** _:LYS_11 2103 10800 0.75 1 21012 21176 1.18 **** _:THR_12 64 648 0.75 1 26340 26340 0.04 _:LEU_13 171 3 0.70 1 15980 15980 0.00 _:LYS_14 2103 6256 0.75 1 19876 19900 0.78 **** _:GLU_16 958 399 0.75 1 12481 12481 0.19 _:THR_17 64 432 0.75 1 26331 26331 0.05 _:THR_18 64 432 0.75 1 26340 26340 0.04 _:THR_19 64 360 0.75 1 26339 26339 0.06 _:VAL_22 17 1 0.70 1 27003 27003 0.01 _:ASP_23 233 22 0.75 1 9517 9517 0.00 _:GLU_25 958 152 0.75 1 12859 12904 0.06 **** _:THR_26 64 72 0.70 1 26338 26338 0.01 _:GLU_28 958 153 0.75 1 12481 12496 0.09 **** _:LYS_29 2103 5563 0.75 1 17048 17048 0.73 _:PHE_31 141 1 0.50 1 26005 26183 0.01 **** _:LYS_32 2103 13586 0.75 1 19880 24108 2.18 **** _:GLN_33 877 342 0.75 1 10567 10567 0.18 _:ASN_36 309 205 0.75 1 8773 8773 0.07 _:ASP_37 233 133 0.75 1 9379 9379 0.02 _:ASN_38 309 154 0.75 1 8793 8793 0.07 _:VAL_40 17 5 0.75 1 26994 26994 0.00 _:ASP_41 233 123 0.75 1 9403 9405 0.01 **** _:VAL_43 17 14 0.75 1 26988 26990 0.00 **** _:TRP_44 168 15 0.50 1 26610 26636 0.02 **** _:THR_45 64 612 0.75 1 26331 26334 0.07 **** _:TYR_46 187 1008 0.75 1 26916 26902 0.07 **** _:ASP_47 233 103 0.75 1 9283 9283 0.03 _:THR_50 64 36 0.70 1 26332 26332 0.00 _:LYS_51 2103 7147 0.75 1 21176 21176 1.02 _:PHE_53 141 2 0.75 1 26013 25961 0.01 **** _:THR_54 64 468 0.75 1 26331 26331 0.07 _:VAL_55 17 3 0.75 1 26988 26997 0.00 **** _:THR_56 64 540 0.75 1 26331 26331 0.06 _:GLU_57 958 548 0.75 1 13723 13729 0.31 **** Time for iteration: 8.679999805986881 Rotamer placement not converged; flips: 19 ------------------------------------------ NOW PICKING ROTAMER STATE BY ENERGY ... (res, # rotamers, # evaluated, ofac, cluster, rot #, old rot #, times) _:VAL_1 17 10 0.75 1 26988 26988 0.01 _:THR_2 64 216 0.75 1 26334 26334 0.03 _:TYR_4 187 144 0.60 1 26776 26776 0.03 _:LEU_6 171 5 0.70 1 16240 15918 0.01 **** _:VAL_7 17 6 0.75 1 26988 26988 0.01 _:ILE_8 178 1 0.75 1 15614 15604 0.00 **** _:ASN_9 309 104 0.75 1 8581 8625 0.04 **** _:LYS_11 2103 10776 0.75 1 21012 21012 1.17 _:THR_12 64 648 0.75 1 26340 26340 0.03 _:LEU_13 171 3 0.70 1 15980 15980 0.00 _:LYS_14 2103 7102 0.75 1 20016 19876 0.87 **** _:GLU_16 958 399 0.75 1 12481 12481 0.19 _:THR_17 64 360 0.75 1 26331 26331 0.05 _:THR_18 64 432 0.75 1 26340 26340 0.04 _:THR_19 64 180 0.65 1 26342 26339 0.03 **** _:VAL_22 17 1 0.70 1 27003 27003 0.00 _:ASP_23 233 22 0.75 1 9517 9517 0.01 _:GLU_25 958 152 0.75 1 12859 12859 0.07 _:THR_26 64 72 0.70 1 26338 26338 0.01 _:GLU_28 958 126 0.75 1 12466 12481 0.08 **** _:LYS_29 2103 5563 0.75 1 17048 17048 0.71 _:PHE_31 141 2 0.50 1 26003 26005 0.01 **** _:LYS_32 2103 11787 0.75 1 20856 19880 1.92 **** _:GLN_33 877 342 0.75 1 10567 10567 0.18 _:ASN_36 309 205 0.75 1 8773 8773 0.07 _:ASP_37 233 133 0.75 1 9379 9379 0.02 _:ASN_38 309 153 0.75 1 8793 8793 0.06 _:VAL_40 17 5 0.75 1 26994 26994 0.00 _:ASP_41 233 123 0.75 1 9403 9403 0.02 _:VAL_43 17 14 0.75 1 26988 26988 0.01 _:TRP_44 168 14 0.75 1 26596 26610 0.02 **** _:THR_45 64 612 0.75 1 26331 26331 0.06 _:TYR_46 187 972 0.75 1 26902 26916 0.07 **** _:ASP_47 233 103 0.75 1 9283 9283 0.02 _:THR_50 64 36 0.70 1 26332 26332 0.01 _:LYS_51 2103 7147 0.75 1 21176 21176 1.02 _:PHE_53 141 4 0.75 1 26013 26013 0.01 _:THR_54 64 468 0.75 1 26331 26331 0.06 _:VAL_55 17 1 0.75 1 27004 26988 0.00 **** _:THR_56 64 540 0.75 1 26331 26331 0.06 _:GLU_57 958 510 0.75 1 13456 13723 0.28 **** Time for iteration: 8.399999812245369 Rotamer placement not converged; flips: 12 ------------------------------------------ NOW PICKING ROTAMER STATE BY ENERGY ... (res, # rotamers, # evaluated, ofac, cluster, rot #, old rot #, times) _:VAL_1 17 10 0.75 1 26988 26988 0.00 _:THR_2 64 216 0.75 1 26334 26334 0.02 _:TYR_4 187 144 0.60 1 26776 26776 0.02 _:LEU_6 171 7 0.60 1 16240 16240 0.01 _:VAL_7 17 6 0.75 1 26988 26988 0.01 _:ILE_8 178 1 0.75 1 15614 15614 0.00 _:ASN_9 309 80 0.75 1 8581 8581 0.03 _:LYS_11 2103 10800 0.75 1 21012 21012 1.17 _:THR_12 64 648 0.75 1 26340 26340 0.03 _:LEU_13 171 3 0.70 1 15980 15980 0.00 _:LYS_14 2103 7102 0.75 1 20016 20016 0.87 _:GLU_16 958 399 0.75 1 12481 12481 0.19 _:THR_17 64 396 0.75 1 26331 26331 0.05 _:THR_18 64 432 0.75 1 26340 26340 0.05 _:THR_19 64 36 0.65 1 26343 26342 0.01 **** _:VAL_22 17 1 0.70 1 27003 27003 0.00 _:ASP_23 233 22 0.75 1 9517 9517 0.01 _:GLU_25 958 152 0.75 1 12859 12859 0.07 _:THR_26 64 72 0.70 1 26338 26338 0.01 _:GLU_28 958 118 0.75 1 12289 12466 0.07 **** _:LYS_29 2103 5563 0.75 1 17048 17048 0.72 _:PHE_31 141 2 0.50 1 26003 26003 0.00 _:LYS_32 2103 12325 0.75 1 20856 20856 2.02 _:GLN_33 877 342 0.75 1 10567 10567 0.18 _:ASN_36 309 205 0.75 1 8773 8773 0.07 _:ASP_37 233 133 0.75 1 9379 9379 0.02 _:ASN_38 309 156 0.75 1 8793 8793 0.07 _:VAL_40 17 5 0.75 1 26994 26994 0.00 _:ASP_41 233 123 0.75 1 9403 9403 0.01 _:VAL_43 17 14 0.75 1 26988 26988 0.00 _:TRP_44 168 14 0.75 1 26614 26596 0.02 **** _:THR_45 64 612 0.75 1 26331 26331 0.07 _:TYR_46 187 972 0.75 1 26902 26902 0.06 _:ASP_47 233 103 0.75 1 9283 9283 0.03 _:THR_50 64 36 0.70 1 26332 26332 0.00 _:LYS_51 2103 7147 0.75 1 21176 21176 1.03 _:PHE_53 141 5 0.75 1 26013 26013 0.01 _:THR_54 64 468 0.75 1 26331 26331 0.07 _:VAL_55 17 1 0.75 1 27004 27004 0.00 _:THR_56 64 540 0.75 1 26331 26331 0.06 _:GLU_57 958 510 0.75 1 13456 13456 0.28 Time for iteration: 8.459999810904264 Rotamer placement not converged; flips: 3 ------------------------------------------ NOW PICKING ROTAMER STATE BY ENERGY ... (res, # rotamers, # evaluated, ofac, cluster, rot #, old rot #, times) _:VAL_1 17 10 0.75 1 26988 26988 0.01 _:THR_2 64 216 0.75 1 26334 26334 0.03 _:TYR_4 187 144 0.60 1 26776 26776 0.03 _:LEU_6 171 7 0.60 1 16240 16240 0.01 _:VAL_7 17 6 0.75 1 26988 26988 0.01 _:ILE_8 178 1 0.75 1 15614 15614 0.00 _:ASN_9 309 80 0.75 1 8581 8581 0.03 _:LYS_11 2103 10800 0.75 1 21012 21012 1.18 _:THR_12 64 648 0.75 1 26340 26340 0.03 _:LEU_13 171 3 0.70 1 15980 15980 0.01 _:LYS_14 2103 7102 0.75 1 20016 20016 0.88 _:GLU_16 958 399 0.75 1 12481 12481 0.20 _:THR_17 64 396 0.75 1 26331 26331 0.05 _:THR_18 64 432 0.75 1 26340 26340 0.04 _:THR_19 64 36 0.65 1 26343 26343 0.01 _:VAL_22 17 1 0.70 1 27003 27003 0.00 _:ASP_23 233 22 0.75 1 9517 9517 0.00 _:GLU_25 958 152 0.75 1 12859 12859 0.06 _:THR_26 64 72 0.70 1 26338 26338 0.01 _:GLU_28 958 118 0.75 1 12289 12289 0.07 _:LYS_29 2103 5563 0.75 1 17048 17048 0.71 _:PHE_31 141 2 0.50 1 26003 26003 0.00 _:LYS_32 2103 13285 0.75 1 20856 20856 2.17 _:GLN_33 877 342 0.75 1 10567 10567 0.17 _:ASN_36 309 205 0.75 1 8773 8773 0.06 _:ASP_37 233 133 0.75 1 9379 9379 0.03 _:ASN_38 309 156 0.75 1 8793 8793 0.06 _:VAL_40 17 5 0.75 1 26994 26994 0.01 _:ASP_41 233 123 0.75 1 9403 9403 0.02 _:VAL_43 17 14 0.75 1 26988 26988 0.01 _:TRP_44 168 14 0.75 1 26614 26614 0.02 _:THR_45 64 612 0.75 1 26331 26331 0.06 _:TYR_46 187 972 0.75 1 26902 26902 0.07 _:ASP_47 233 103 0.75 1 9283 9283 0.02 _:THR_50 64 36 0.70 1 26332 26332 0.00 _:LYS_51 2103 7147 0.75 1 21176 21176 1.03 _:PHE_53 141 5 0.75 1 26013 26013 0.01 _:THR_54 64 468 0.75 1 26331 26331 0.06 _:VAL_55 17 1 0.75 1 27004 27004 0.00 _:THR_56 64 540 0.75 1 26331 26331 0.06 _:GLU_57 958 510 0.75 1 13456 13456 0.28 Time for iteration: 8.629999807104468 Current RMSDs: Aligned res, calpha/ 56 5.35 Aligned res, calpha/ 168 5.55 Aligned res, calpha/ 446 5.72 All res, calpha/calp 57 5.35 All res, calpha/back 171 5.55 All res, calpha/heav 457 5.72 ============================================= Now minimizing non-template regions ... ============================================= COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 42.274239 115.457414 183.120493 340.852145 SGB 6119.756041 -2743.212915 -2312.749782 1063.793344 TOTAL 6162.030280 -2627.755501 -2129.629290 1404.645490 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 399.323068 -144.398378 -12.752096 242.172593 EL 1973.522436 -4215.912262 72.596452 -2169.793374 SGB -2312.749782 2756.053439 -83.819470 359.484186 TOTAL 60.095722 -1604.257202 -23.975114 -1568.136594 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4788.730218 NONPOLAR 8.137034 SGB TOT -1052.702905 SOLV TOT -1044.565871 TOTALE -2631.334506 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 22.600634 102.792974 168.500727 293.894334 SGB 6095.458576 -2735.437293 -2299.921458 1060.099826 TOTAL 6118.059210 -2632.644319 -2131.420731 1353.994160 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 328.301318 -276.088824 -12.989482 39.223012 EL 1967.704933 -4262.553331 102.194183 -2192.654215 SGB -2299.921458 2776.966500 -113.446858 363.598184 TOTAL -3.915207 -1761.675655 -24.242156 -1789.833018 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4767.559188 NONPOLAR 8.785958 SGB TOT -1043.939721 SOLV TOT -1035.153763 TOTALE -2894.690631 Current RMSDs: Aligned res, calpha/ 56 5.32 Aligned res, calpha/ 168 5.54 Aligned res, calpha/ 446 5.73 All res, calpha/calp 57 5.32 All res, calpha/back 171 5.54 All res, calpha/heav 457 5.73 COVALENT ENERGIES: BOND ANGLE TOR TOTAL COV 22.600634 102.792974 168.500727 293.894334 SGB 6095.458576 -2735.437293 -2299.921458 1060.099826 TOTAL 6118.059210 -2632.644319 -2131.420731 1353.994160 TIME 0.000000 0.000000 0.000000 0.000000 NONBONDED (INTRAMOLECULAR) ENERGIES: 14 SHORT LONG TOTAL LJ 328.301318 -276.088824 -16.996372 35.216123 EL 1967.704933 -4262.553331 3004.732498 709.884100 SGB -2299.921458 5218.911387 -2964.638440 -45.648511 TOTAL -3.915207 680.269233 23.097686 699.451712 TIME 0.000000 0.000000 0.000000 0.000000 OTHER: SGB SELF -4767.559188 NONPOLAR 8.785958 SGB TOT -1453.186416 SOLV TOT -1444.400458 TOTALE -405.405901 WARNING: above phi/psi not represented by library GENback Actual angles 150.00 -153.97 Closest rotamer -175.00 -180.00 Delta 35.00 -26.03 Problems have been detected for _:ALA_21 The phi/psi angles do not correspond to allowed region of Ramachandran plot (as defined by the rotamer library) phi: 150.00 psi: -153.97 WARNING: above phi/psi not represented by library GENback Actual angles -141.90 -89.30 Closest rotamer -115.00 -70.00 Delta 26.90 19.30 Problems have been detected for _:THR_26 The phi/psi angles do not correspond to allowed region of Ramachandran plot (as defined by the rotamer library) phi: -141.90 psi: -89.30 WARNING: above phi/psi not represented by library GENback Actual angles 101.01 -8.57 Closest rotamer 75.00 5.00 Delta -26.01 13.57 Problems have been detected for _:THR_50 The phi/psi angles do not correspond to allowed region of Ramachandran plot (as defined by the rotamer library) phi: 101.01 psi: -8.57 A more stringent (and time consuming) test comes from adding side chains to the complete structure. To do so, use command *side pred*. TOTAL TIME ELAPSED: plop_job 123.0099972505122