Starting phenix.real_space_refine on Mon Sep 14 00:55:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w0a_32236/09_2026/7w0a_32236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0a_32236/09_2026/7w0a_32236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w0a_32236/09_2026/7w0a_32236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0a_32236/09_2026/7w0a_32236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0a_32236/09_2026/7w0a_32236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0a_32236/09_2026/7w0a_32236.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w0a_32236/09_2026/7w0a_32236.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w0a_32236/09_2026/7w0a_32236.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 124 5.49 5 S 124 5.16 5 C 16744 2.51 5 N 4598 2.21 5 O 5308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26898 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11988 Classifications: {'peptide': 1478} Link IDs: {'PTRANS': 61, 'TRANS': 1416} Chain breaks: 2 Chain: "B" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 645 Classifications: {'DNA': 1, 'RNAv2': 30} Modifications used: {'5*END': 1, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna3p': 30} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 672 Classifications: {'RNAv2': 32} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna3p': 31} Chain: "F" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "G" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 645 Classifications: {'DNA': 1, 'RNAv2': 30} Modifications used: {'5*END': 1, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna3p': 30} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 672 Classifications: {'RNAv2': 32} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna3p': 31} Chain: "E" Number of atoms: 11988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1478, 11988 Classifications: {'peptide': 1478} Link IDs: {'PTRANS': 61, 'TRANS': 1416} Chain breaks: 2 Time building chain proxies: 6.06, per 1000 atoms: 0.23 Number of scatterers: 26898 At special positions: 0 Unit cell: (243.843, 177.243, 97.7522, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 124 15.00 O 5308 8.00 N 4598 7.00 C 16744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 20 sheets defined 55.4% alpha, 10.0% beta 44 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.741A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 45 removed outlier: 3.752A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 97 removed outlier: 5.928A pdb=" N VAL A 94 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP A 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.573A pdb=" N GLU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.674A pdb=" N LYS A 164 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 165' Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.686A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 232 through 250 removed outlier: 3.625A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 3.655A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.561A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.802A pdb=" N ASP A 348 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.875A pdb=" N GLU A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.778A pdb=" N ILE A 386 " --> pdb=" O PRO A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.633A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 510 through 535 Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.559A pdb=" N PHE A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 580 Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 608 through 611 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 667 through 680 removed outlier: 3.761A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 687 removed outlier: 3.732A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.706A pdb=" N ALA A 697 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.865A pdb=" N GLN A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.697A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 removed outlier: 4.333A pdb=" N GLN A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 869 " --> pdb=" O GLN A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.533A pdb=" N PHE A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 930 removed outlier: 6.708A pdb=" N ASN A 927 " --> pdb=" O SER A 923 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.919A pdb=" N MET A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 983 through 991 removed outlier: 4.027A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 removed outlier: 3.727A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 removed outlier: 3.530A pdb=" N SER A1182 " --> pdb=" O GLN A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1186 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.879A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 Processing helix chain 'A' and resid 1249 through 1259 Processing helix chain 'A' and resid 1260 through 1261 No H-bonds generated for 'chain 'A' and resid 1260 through 1261' Processing helix chain 'A' and resid 1262 through 1266 removed outlier: 3.985A pdb=" N LEU A1266 " --> pdb=" O PRO A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1277 removed outlier: 3.823A pdb=" N TRP A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1294 Processing helix chain 'A' and resid 1303 through 1308 Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1337 Processing helix chain 'A' and resid 1338 through 1340 No H-bonds generated for 'chain 'A' and resid 1338 through 1340' Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1363 through 1393 removed outlier: 8.103A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS A1388 " --> pdb=" O GLN A1384 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A1389 " --> pdb=" O HIS A1385 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A1390 " --> pdb=" O ALA A1386 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A1391 " --> pdb=" O PHE A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1410 removed outlier: 3.561A pdb=" N LEU A1407 " --> pdb=" O LEU A1404 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A1408 " --> pdb=" O THR A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.985A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.761A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1521 through 1525 removed outlier: 3.601A pdb=" N ILE A1525 " --> pdb=" O HIS A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 removed outlier: 3.508A pdb=" N GLN A1546 " --> pdb=" O PHE A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.172A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1649 Proline residue: A1643 - end of helix Processing helix chain 'E' and resid 9 through 22 removed outlier: 3.741A pdb=" N LYS E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 45 removed outlier: 3.773A pdb=" N THR E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 Processing helix chain 'E' and resid 66 through 81 Processing helix chain 'E' and resid 89 through 97 removed outlier: 5.927A pdb=" N VAL E 94 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 109 removed outlier: 3.561A pdb=" N GLU E 105 " --> pdb=" O MET E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.676A pdb=" N LYS E 164 " --> pdb=" O ASN E 161 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 161 through 165' Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.691A pdb=" N LYS E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 212 Processing helix chain 'E' and resid 232 through 250 removed outlier: 3.625A pdb=" N ARG E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 292 removed outlier: 3.655A pdb=" N VAL E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 314 removed outlier: 3.553A pdb=" N ILE E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 343 Processing helix chain 'E' and resid 344 through 348 removed outlier: 3.804A pdb=" N ASP E 348 " --> pdb=" O THR E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 362 removed outlier: 3.886A pdb=" N GLU E 356 " --> pdb=" O ASN E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 378 Processing helix chain 'E' and resid 382 through 386 removed outlier: 3.778A pdb=" N ILE E 386 " --> pdb=" O PRO E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 410 removed outlier: 3.633A pdb=" N CYS E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 452 Processing helix chain 'E' and resid 484 through 493 Processing helix chain 'E' and resid 510 through 535 Processing helix chain 'E' and resid 543 through 552 removed outlier: 3.575A pdb=" N PHE E 551 " --> pdb=" O ILE E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 570 through 580 Processing helix chain 'E' and resid 598 through 607 Processing helix chain 'E' and resid 608 through 611 Processing helix chain 'E' and resid 637 through 656 Processing helix chain 'E' and resid 667 through 680 removed outlier: 3.762A pdb=" N ILE E 675 " --> pdb=" O ARG E 671 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP E 677 " --> pdb=" O ALA E 673 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL E 678 " --> pdb=" O SER E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 687 removed outlier: 3.730A pdb=" N LYS E 685 " --> pdb=" O HIS E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 693 through 697 removed outlier: 3.709A pdb=" N ALA E 697 " --> pdb=" O VAL E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 749 removed outlier: 3.862A pdb=" N GLN E 749 " --> pdb=" O TYR E 745 " (cutoff:3.500A) Processing helix chain 'E' and resid 792 through 810 removed outlier: 3.695A pdb=" N PHE E 807 " --> pdb=" O HIS E 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 845 through 852 removed outlier: 3.658A pdb=" N MET E 849 " --> pdb=" O ASP E 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 862 through 869 removed outlier: 4.333A pdb=" N GLN E 868 " --> pdb=" O GLN E 864 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 869 " --> pdb=" O GLN E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 878 removed outlier: 3.533A pdb=" N PHE E 877 " --> pdb=" O ARG E 873 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 930 removed outlier: 6.712A pdb=" N ASN E 927 " --> pdb=" O SER E 923 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG E 928 " --> pdb=" O LYS E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 960 through 967 removed outlier: 3.919A pdb=" N MET E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 972 through 974 No H-bonds generated for 'chain 'E' and resid 972 through 974' Processing helix chain 'E' and resid 983 through 991 removed outlier: 4.019A pdb=" N PHE E 991 " --> pdb=" O LEU E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 991 through 1016 removed outlier: 3.727A pdb=" N PHE E1001 " --> pdb=" O ASN E 997 " (cutoff:3.500A) Processing helix chain 'E' and resid 1174 through 1182 removed outlier: 3.530A pdb=" N SER E1182 " --> pdb=" O GLN E1178 " (cutoff:3.500A) Processing helix chain 'E' and resid 1183 through 1186 Processing helix chain 'E' and resid 1190 through 1199 Processing helix chain 'E' and resid 1209 through 1232 removed outlier: 3.881A pdb=" N LEU E1215 " --> pdb=" O ARG E1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 1236 through 1248 Processing helix chain 'E' and resid 1249 through 1259 Processing helix chain 'E' and resid 1260 through 1261 No H-bonds generated for 'chain 'E' and resid 1260 through 1261' Processing helix chain 'E' and resid 1262 through 1266 removed outlier: 3.984A pdb=" N LEU E1266 " --> pdb=" O PRO E1263 " (cutoff:3.500A) Processing helix chain 'E' and resid 1272 through 1277 removed outlier: 3.822A pdb=" N TRP E1277 " --> pdb=" O PRO E1273 " (cutoff:3.500A) Processing helix chain 'E' and resid 1285 through 1294 Processing helix chain 'E' and resid 1303 through 1308 Processing helix chain 'E' and resid 1313 through 1319 Processing helix chain 'E' and resid 1324 through 1337 Processing helix chain 'E' and resid 1338 through 1340 No H-bonds generated for 'chain 'E' and resid 1338 through 1340' Processing helix chain 'E' and resid 1348 through 1353 Processing helix chain 'E' and resid 1354 through 1356 No H-bonds generated for 'chain 'E' and resid 1354 through 1356' Processing helix chain 'E' and resid 1363 through 1393 removed outlier: 8.111A pdb=" N LEU E1383 " --> pdb=" O LYS E1379 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N GLN E1384 " --> pdb=" O ASN E1380 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS E1385 " --> pdb=" O TYR E1381 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS E1388 " --> pdb=" O GLN E1384 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E1389 " --> pdb=" O HIS E1385 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU E1390 " --> pdb=" O ALA E1386 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU E1391 " --> pdb=" O PHE E1387 " (cutoff:3.500A) Processing helix chain 'E' and resid 1403 through 1410 removed outlier: 3.563A pdb=" N LEU E1407 " --> pdb=" O LEU E1404 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU E1408 " --> pdb=" O THR E1405 " (cutoff:3.500A) Processing helix chain 'E' and resid 1422 through 1430 removed outlier: 3.986A pdb=" N ILE E1426 " --> pdb=" O ASN E1422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE E1429 " --> pdb=" O GLU E1425 " (cutoff:3.500A) Processing helix chain 'E' and resid 1432 through 1441 Processing helix chain 'E' and resid 1447 through 1455 Processing helix chain 'E' and resid 1468 through 1491 removed outlier: 3.762A pdb=" N ILE E1474 " --> pdb=" O GLU E1470 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA E1477 " --> pdb=" O PHE E1473 " (cutoff:3.500A) Processing helix chain 'E' and resid 1495 through 1507 Processing helix chain 'E' and resid 1508 through 1519 Processing helix chain 'E' and resid 1521 through 1525 removed outlier: 3.599A pdb=" N ILE E1525 " --> pdb=" O HIS E1522 " (cutoff:3.500A) Processing helix chain 'E' and resid 1529 through 1546 removed outlier: 3.510A pdb=" N GLN E1546 " --> pdb=" O PHE E1542 " (cutoff:3.500A) Processing helix chain 'E' and resid 1609 through 1628 removed outlier: 4.177A pdb=" N GLY E1613 " --> pdb=" O PRO E1609 " (cutoff:3.500A) Processing helix chain 'E' and resid 1629 through 1649 Proline residue: E1643 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.822A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR A 115 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR A 88 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 25 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 424 removed outlier: 6.608A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR A 219 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU A 504 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 221 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR A 506 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 223 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.658A pdb=" N ARG A 260 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 772 Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 772 removed outlier: 4.616A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB1, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.415A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET A 939 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL A 898 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU A 941 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 357 through 358 removed outlier: 6.232A pdb=" N THR E 219 " --> pdb=" O PHE E 502 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU E 504 " --> pdb=" O THR E 219 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL E 221 " --> pdb=" O LEU E 504 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR E 506 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL E 223 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU E 389 " --> pdb=" O PHE E 477 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN E 422 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 88 removed outlier: 5.825A pdb=" N GLY E 86 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N THR E 115 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR E 88 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG E 59 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL E 136 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU E 61 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE E 138 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N MET E 63 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE E 25 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 260 through 261 removed outlier: 4.659A pdb=" N ARG E 260 " --> pdb=" O ARG E 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AB6, first strand: chain 'E' and resid 593 through 596 Processing sheet with id=AB7, first strand: chain 'E' and resid 702 through 706 Processing sheet with id=AB8, first strand: chain 'E' and resid 768 through 772 Processing sheet with id=AB9, first strand: chain 'E' and resid 768 through 772 removed outlier: 4.620A pdb=" N TYR E 754 " --> pdb=" O ILE E 729 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 819 through 820 Processing sheet with id=AC2, first strand: chain 'E' and resid 969 through 971 removed outlier: 4.406A pdb=" N VAL E 969 " --> pdb=" O VAL E 942 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET E 939 " --> pdb=" O VAL E 898 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL E 898 " --> pdb=" O MET E 939 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLU E 941 " --> pdb=" O THR E 896 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS E 880 " --> pdb=" O VAL E 895 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE E 881 " --> pdb=" O PHE E 979 " (cutoff:3.500A) 1161 hydrogen bonds defined for protein. 3288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 7.33 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7453 1.33 - 1.45: 5253 1.45 - 1.57: 14580 1.57 - 1.69: 246 1.69 - 1.81: 194 Bond restraints: 27726 Sorted by residual: bond pdb=" CB CYS E 400 " pdb=" SG CYS E 400 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.41e+00 bond pdb=" CB CYS A 400 " pdb=" SG CYS A 400 " ideal model delta sigma weight residual 1.808 1.770 0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" CA SER E 461 " pdb=" CB SER E 461 " ideal model delta sigma weight residual 1.527 1.500 0.027 2.48e-02 1.63e+03 1.19e+00 bond pdb=" CA SER A 461 " pdb=" CB SER A 461 " ideal model delta sigma weight residual 1.527 1.500 0.027 2.48e-02 1.63e+03 1.19e+00 bond pdb=" CA MET A 967 " pdb=" CB MET A 967 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.41e-02 5.03e+03 1.16e+00 ... (remaining 27721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 37335 1.81 - 3.62: 713 3.62 - 5.43: 47 5.43 - 7.24: 6 7.24 - 9.05: 1 Bond angle restraints: 38102 Sorted by residual: angle pdb=" CB MET A 360 " pdb=" CG MET A 360 " pdb=" SD MET A 360 " ideal model delta sigma weight residual 112.70 121.75 -9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C LYS A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.96e+00 angle pdb=" C LYS E 539 " pdb=" N THR E 540 " pdb=" CA THR E 540 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.57e+00 angle pdb=" C MET E 344 " pdb=" N THR E 345 " pdb=" CA THR E 345 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.41e+00 angle pdb=" C MET A 344 " pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.39e+00 ... (remaining 38097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14875 17.98 - 35.95: 1253 35.95 - 53.93: 280 53.93 - 71.90: 50 71.90 - 89.88: 34 Dihedral angle restraints: 16492 sinusoidal: 7682 harmonic: 8810 Sorted by residual: dihedral pdb=" CA LEU E 758 " pdb=" C LEU E 758 " pdb=" N ARG E 759 " pdb=" CA ARG E 759 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N ARG A 759 " pdb=" CA ARG A 759 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASP E1261 " pdb=" CB ASP E1261 " pdb=" CG ASP E1261 " pdb=" OD1 ASP E1261 " ideal model delta sinusoidal sigma weight residual -30.00 -87.80 57.80 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 16489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3406 0.050 - 0.099: 708 0.099 - 0.149: 132 0.149 - 0.198: 4 0.198 - 0.248: 124 Chirality restraints: 4374 Sorted by residual: chirality pdb=" P G G 1 " pdb=" OP1 G G 1 " pdb=" OP2 G G 1 " pdb=" O5' G G 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" P G C 1 " pdb=" OP1 G C 1 " pdb=" OP2 G C 1 " pdb=" O5' G C 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" P G G 24 " pdb=" OP1 G G 24 " pdb=" OP2 G G 24 " pdb=" O5' G G 24 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4371 not shown) Planarity restraints: 4426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 344 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C MET A 344 " 0.031 2.00e-02 2.50e+03 pdb=" O MET A 344 " -0.011 2.00e-02 2.50e+03 pdb=" N THR A 345 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A1456 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A1457 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1457 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1457 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 344 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C MET E 344 " 0.030 2.00e-02 2.50e+03 pdb=" O MET E 344 " -0.011 2.00e-02 2.50e+03 pdb=" N THR E 345 " -0.010 2.00e-02 2.50e+03 ... (remaining 4423 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1668 2.73 - 3.27: 27277 3.27 - 3.81: 45404 3.81 - 4.36: 55814 4.36 - 4.90: 91109 Nonbonded interactions: 221272 Sorted by model distance: nonbonded pdb=" O VAL E 437 " pdb=" NH1 ARG E 440 " model vdw 2.186 3.120 nonbonded pdb=" O VAL A 437 " pdb=" NH1 ARG A 440 " model vdw 2.195 3.120 nonbonded pdb=" NZ LYS A 340 " pdb=" OD1 ASP B 345 " model vdw 2.205 3.120 nonbonded pdb=" O2 C G 11 " pdb=" N2 G H 40 " model vdw 2.220 3.120 nonbonded pdb=" O2 C C 11 " pdb=" N2 G D 40 " model vdw 2.221 3.120 ... (remaining 221267 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 29.620 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27726 Z= 0.161 Angle : 0.577 9.054 38102 Z= 0.297 Chirality : 0.056 0.248 4374 Planarity : 0.004 0.056 4426 Dihedral : 14.233 89.877 10780 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 2972 helix: 1.04 (0.14), residues: 1416 sheet: -0.07 (0.31), residues: 302 loop : -0.05 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 764 TYR 0.017 0.001 TYR A1468 PHE 0.026 0.002 PHE E 818 TRP 0.020 0.002 TRP A1235 HIS 0.008 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (27726) covalent geometry : angle 0.57708 / 0.30 (38102) hydrogen bonds : bond 0.17092 / 11.21 ( 1247) hydrogen bonds : angle 6.87431 / 4.93 ( 3500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.778 Fit side-chains REVERT: A 214 TYR cc_start: 0.8800 (p90) cc_final: 0.8153 (p90) REVERT: A 324 ARG cc_start: 0.6857 (mmm160) cc_final: 0.6650 (ttm-80) REVERT: A 527 ASP cc_start: 0.8056 (m-30) cc_final: 0.7697 (m-30) REVERT: A 548 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8118 (tptp) REVERT: E 324 ARG cc_start: 0.6861 (mmm160) cc_final: 0.6656 (ttm-80) REVERT: E 342 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7379 (mt0) REVERT: E 362 PHE cc_start: 0.8852 (m-80) cc_final: 0.8441 (m-10) REVERT: E 527 ASP cc_start: 0.8056 (m-30) cc_final: 0.7697 (m-30) REVERT: E 548 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8135 (tptp) REVERT: E 920 PHE cc_start: 0.8460 (t80) cc_final: 0.8228 (t80) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1980 time to fit residues: 105.6284 Evaluate side-chains 221 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1217 ASN A1406 GLN A1491 ASN E 800 HIS E1406 GLN E1491 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103613 restraints weight = 35817.261| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.18 r_work: 0.3115 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27726 Z= 0.119 Angle : 0.550 5.624 38102 Z= 0.272 Chirality : 0.044 0.228 4374 Planarity : 0.004 0.040 4426 Dihedral : 8.404 61.382 4736 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.00 % Allowed : 6.13 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 2972 helix: 1.21 (0.14), residues: 1454 sheet: -0.38 (0.29), residues: 316 loop : 0.10 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 866 TYR 0.017 0.001 TYR E1000 PHE 0.013 0.001 PHE A 818 TRP 0.010 0.001 TRP E 986 HIS 0.002 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (27726) covalent geometry : angle 0.54959 / 0.27 (38102) hydrogen bonds : bond 0.04528 / 3.04 ( 1247) hydrogen bonds : angle 4.44867 / 3.19 ( 3500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.996 Fit side-chains REVERT: A 102 TRP cc_start: 0.8469 (m100) cc_final: 0.8018 (m100) REVERT: A 106 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 214 TYR cc_start: 0.8840 (p90) cc_final: 0.8120 (p90) REVERT: A 458 MET cc_start: 0.9072 (tpp) cc_final: 0.8864 (tpt) REVERT: A 527 ASP cc_start: 0.8423 (m-30) cc_final: 0.7943 (m-30) REVERT: A 548 LYS cc_start: 0.8337 (ttpt) cc_final: 0.7778 (tptp) REVERT: A 552 GLN cc_start: 0.7665 (pp30) cc_final: 0.7203 (pp30) REVERT: A 794 GLU cc_start: 0.8342 (pm20) cc_final: 0.7855 (tp30) REVERT: A 873 ARG cc_start: 0.8274 (mpp80) cc_final: 0.7982 (ptp-170) REVERT: A 1493 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8539 (mtmt) REVERT: E 102 TRP cc_start: 0.8470 (m100) cc_final: 0.8035 (m100) REVERT: E 106 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8391 (mp) REVERT: E 360 MET cc_start: 0.8467 (mmt) cc_final: 0.8137 (mmm) REVERT: E 458 MET cc_start: 0.9076 (tpp) cc_final: 0.8861 (tpt) REVERT: E 527 ASP cc_start: 0.8405 (m-30) cc_final: 0.7923 (m-30) REVERT: E 548 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7762 (tptp) REVERT: E 794 GLU cc_start: 0.8311 (pm20) cc_final: 0.7841 (tp30) REVERT: E 821 ASP cc_start: 0.8222 (t70) cc_final: 0.7692 (t0) REVERT: E 873 ARG cc_start: 0.8260 (mpp80) cc_final: 0.7968 (ptp-170) REVERT: E 1493 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8537 (mtmt) outliers start: 27 outliers final: 16 residues processed: 250 average time/residue: 0.1766 time to fit residues: 71.7959 Evaluate side-chains 220 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1038 SER Chi-restraints excluded: chain E residue 1314 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 129 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 304 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 217 optimal weight: 0.0980 chunk 87 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102907 restraints weight = 35621.362| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.33 r_work: 0.3103 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27726 Z= 0.112 Angle : 0.516 6.256 38102 Z= 0.255 Chirality : 0.044 0.208 4374 Planarity : 0.004 0.040 4426 Dihedral : 8.153 60.322 4736 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.00 % Allowed : 7.99 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 2972 helix: 1.27 (0.14), residues: 1452 sheet: -0.52 (0.28), residues: 320 loop : 0.09 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 346 TYR 0.017 0.001 TYR A1000 PHE 0.017 0.001 PHE E1542 TRP 0.009 0.001 TRP E 986 HIS 0.002 0.001 HIS E1456 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (27726) covalent geometry : angle 0.51550 / 0.26 (38102) hydrogen bonds : bond 0.03837 / 2.61 ( 1247) hydrogen bonds : angle 4.08063 / 2.92 ( 3500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.097 Fit side-chains REVERT: A 102 TRP cc_start: 0.8402 (m100) cc_final: 0.8073 (m100) REVERT: A 106 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 527 ASP cc_start: 0.8484 (m-30) cc_final: 0.7999 (m-30) REVERT: A 548 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7795 (tptp) REVERT: A 552 GLN cc_start: 0.7753 (pp30) cc_final: 0.7319 (pp30) REVERT: A 794 GLU cc_start: 0.8300 (pm20) cc_final: 0.7877 (tp30) REVERT: A 873 ARG cc_start: 0.8262 (mpp80) cc_final: 0.7964 (ptp-170) REVERT: A 970 ILE cc_start: 0.8686 (mm) cc_final: 0.8374 (mp) REVERT: A 1493 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8505 (mtmt) REVERT: E 102 TRP cc_start: 0.8429 (m100) cc_final: 0.7975 (m100) REVERT: E 122 MET cc_start: 0.8589 (ttp) cc_final: 0.8079 (ttp) REVERT: E 344 MET cc_start: 0.6654 (ttp) cc_final: 0.6087 (ttp) REVERT: E 527 ASP cc_start: 0.8487 (m-30) cc_final: 0.8000 (m-30) REVERT: E 548 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7773 (tptp) REVERT: E 794 GLU cc_start: 0.8294 (pm20) cc_final: 0.7873 (tp30) REVERT: E 821 ASP cc_start: 0.8262 (t70) cc_final: 0.7728 (t0) REVERT: E 873 ARG cc_start: 0.8237 (mpp80) cc_final: 0.7939 (ptp-170) REVERT: E 1493 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8509 (mtmt) outliers start: 27 outliers final: 17 residues processed: 232 average time/residue: 0.1801 time to fit residues: 68.2483 Evaluate side-chains 215 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 487 MET Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1038 SER Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 216 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 179 optimal weight: 0.3980 chunk 219 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 158 optimal weight: 50.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100962 restraints weight = 35542.255| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.30 r_work: 0.3061 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27726 Z= 0.150 Angle : 0.534 6.054 38102 Z= 0.266 Chirality : 0.044 0.196 4374 Planarity : 0.004 0.043 4426 Dihedral : 8.130 58.290 4736 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.23 % Allowed : 9.18 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 2972 helix: 1.22 (0.14), residues: 1446 sheet: -0.60 (0.28), residues: 330 loop : 0.03 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 346 TYR 0.019 0.001 TYR A1000 PHE 0.012 0.001 PHE E 362 TRP 0.009 0.001 TRP E 986 HIS 0.004 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (27726) covalent geometry : angle 0.53407 / 0.27 (38102) hydrogen bonds : bond 0.04114 / 2.81 ( 1247) hydrogen bonds : angle 4.11626 / 2.94 ( 3500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 1.191 Fit side-chains REVERT: A 102 TRP cc_start: 0.8479 (m100) cc_final: 0.8200 (m100) REVERT: A 527 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: A 548 LYS cc_start: 0.8446 (ttpt) cc_final: 0.7890 (tptp) REVERT: A 794 GLU cc_start: 0.8313 (pm20) cc_final: 0.7957 (tp30) REVERT: A 873 ARG cc_start: 0.8276 (mpp80) cc_final: 0.7968 (ptp-170) REVERT: A 1493 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8556 (mtmt) REVERT: E 344 MET cc_start: 0.6689 (ttp) cc_final: 0.6003 (ttp) REVERT: E 527 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: E 548 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7867 (tptp) REVERT: E 794 GLU cc_start: 0.8322 (pm20) cc_final: 0.7998 (tp30) REVERT: E 873 ARG cc_start: 0.8256 (mpp80) cc_final: 0.7949 (ptp-170) REVERT: E 918 TYR cc_start: 0.8411 (t80) cc_final: 0.8104 (t80) REVERT: E 1493 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8553 (mtmt) outliers start: 33 outliers final: 19 residues processed: 226 average time/residue: 0.1775 time to fit residues: 65.5923 Evaluate side-chains 216 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 487 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1400 ILE Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 168 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 257 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 147 optimal weight: 0.3980 chunk 187 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101939 restraints weight = 35477.375| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.25 r_work: 0.3087 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27726 Z= 0.112 Angle : 0.504 6.155 38102 Z= 0.251 Chirality : 0.043 0.190 4374 Planarity : 0.003 0.042 4426 Dihedral : 8.128 58.695 4736 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.19 % Allowed : 10.22 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 2972 helix: 1.26 (0.14), residues: 1458 sheet: -0.63 (0.28), residues: 320 loop : 0.06 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 346 TYR 0.016 0.001 TYR E1000 PHE 0.016 0.001 PHE E1542 TRP 0.009 0.001 TRP A1634 HIS 0.002 0.000 HIS A1456 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (27726) covalent geometry : angle 0.50391 / 0.25 (38102) hydrogen bonds : bond 0.03730 / 2.54 ( 1247) hydrogen bonds : angle 4.00446 / 2.86 ( 3500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.876 Fit side-chains REVERT: A 102 TRP cc_start: 0.8380 (m100) cc_final: 0.8074 (m100) REVERT: A 527 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: A 548 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7805 (tptp) REVERT: A 794 GLU cc_start: 0.8355 (pm20) cc_final: 0.7935 (tp30) REVERT: A 873 ARG cc_start: 0.8198 (mpp80) cc_final: 0.7894 (ptp-170) REVERT: A 918 TYR cc_start: 0.8411 (t80) cc_final: 0.8117 (t80) REVERT: A 954 HIS cc_start: 0.7646 (t-90) cc_final: 0.7385 (t-90) REVERT: A 1493 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8512 (mtmt) REVERT: A 1534 GLU cc_start: 0.7512 (tt0) cc_final: 0.7232 (tt0) REVERT: E 102 TRP cc_start: 0.8406 (m100) cc_final: 0.8103 (m100) REVERT: E 344 MET cc_start: 0.6606 (ttp) cc_final: 0.5996 (ttp) REVERT: E 527 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: E 548 LYS cc_start: 0.8364 (ttpt) cc_final: 0.7848 (tptp) REVERT: E 794 GLU cc_start: 0.8352 (pm20) cc_final: 0.7984 (tp30) REVERT: E 821 ASP cc_start: 0.8354 (t70) cc_final: 0.7828 (t0) REVERT: E 873 ARG cc_start: 0.8171 (mpp80) cc_final: 0.7863 (ptp-170) REVERT: E 918 TYR cc_start: 0.8377 (t80) cc_final: 0.8127 (t80) REVERT: E 1493 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8513 (mtmt) outliers start: 32 outliers final: 23 residues processed: 233 average time/residue: 0.1758 time to fit residues: 66.9619 Evaluate side-chains 228 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 487 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 1400 ILE Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 120 optimal weight: 0.8980 chunk 301 optimal weight: 8.9990 chunk 193 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 157 optimal weight: 50.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.146322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099771 restraints weight = 35447.905| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.35 r_work: 0.3062 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27726 Z= 0.134 Angle : 0.515 6.453 38102 Z= 0.257 Chirality : 0.043 0.168 4374 Planarity : 0.004 0.043 4426 Dihedral : 8.147 58.950 4736 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.38 % Allowed : 10.67 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 2972 helix: 1.21 (0.14), residues: 1458 sheet: -0.69 (0.27), residues: 330 loop : 0.06 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 346 TYR 0.018 0.001 TYR E1000 PHE 0.012 0.001 PHE E1481 TRP 0.009 0.001 TRP A1634 HIS 0.003 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (27726) covalent geometry : angle 0.51466 / 0.26 (38102) hydrogen bonds : bond 0.03894 / 2.66 ( 1247) hydrogen bonds : angle 4.02530 / 2.87 ( 3500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 1.017 Fit side-chains REVERT: A 527 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: A 548 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7793 (tptp) REVERT: A 794 GLU cc_start: 0.8353 (pm20) cc_final: 0.7999 (tp30) REVERT: A 873 ARG cc_start: 0.8225 (mpp80) cc_final: 0.7933 (mpp80) REVERT: A 918 TYR cc_start: 0.8416 (t80) cc_final: 0.8153 (t80) REVERT: A 1493 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8496 (mtmt) REVERT: A 1534 GLU cc_start: 0.7552 (tt0) cc_final: 0.7270 (tt0) REVERT: E 102 TRP cc_start: 0.8464 (m100) cc_final: 0.8125 (m100) REVERT: E 433 ASP cc_start: 0.8536 (p0) cc_final: 0.8253 (p0) REVERT: E 527 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: E 548 LYS cc_start: 0.8385 (ttpt) cc_final: 0.7846 (tptp) REVERT: E 794 GLU cc_start: 0.8373 (pm20) cc_final: 0.8017 (tp30) REVERT: E 873 ARG cc_start: 0.8195 (mpp80) cc_final: 0.7910 (mpp80) REVERT: E 918 TYR cc_start: 0.8399 (t80) cc_final: 0.8169 (t80) REVERT: E 1493 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8495 (mtmt) REVERT: E 1534 GLU cc_start: 0.7553 (tt0) cc_final: 0.7266 (tt0) outliers start: 37 outliers final: 27 residues processed: 234 average time/residue: 0.1782 time to fit residues: 67.7276 Evaluate side-chains 229 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 487 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 166 optimal weight: 0.0470 chunk 303 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 277 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102196 restraints weight = 35281.538| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.38 r_work: 0.3102 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27726 Z= 0.105 Angle : 0.495 6.905 38102 Z= 0.246 Chirality : 0.042 0.169 4374 Planarity : 0.003 0.042 4426 Dihedral : 8.129 58.881 4736 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.52 % Allowed : 10.93 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 2972 helix: 1.31 (0.14), residues: 1456 sheet: -0.67 (0.28), residues: 312 loop : 0.07 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 346 TYR 0.016 0.001 TYR A1000 PHE 0.017 0.001 PHE E 362 TRP 0.021 0.001 TRP A 102 HIS 0.002 0.000 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (27726) covalent geometry : angle 0.49464 / 0.25 (38102) hydrogen bonds : bond 0.03559 / 2.43 ( 1247) hydrogen bonds : angle 3.92916 / 2.80 ( 3500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 1.003 Fit side-chains REVERT: A 527 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: A 548 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7800 (tptp) REVERT: A 794 GLU cc_start: 0.8271 (pm20) cc_final: 0.7981 (tp30) REVERT: A 873 ARG cc_start: 0.8211 (mpp80) cc_final: 0.7906 (mpp80) REVERT: A 1534 GLU cc_start: 0.7553 (tt0) cc_final: 0.7283 (tt0) REVERT: E 102 TRP cc_start: 0.8412 (m100) cc_final: 0.8054 (m100) REVERT: E 433 ASP cc_start: 0.8548 (p0) cc_final: 0.8261 (p0) REVERT: E 527 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: E 548 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7874 (tptp) REVERT: E 794 GLU cc_start: 0.8314 (pm20) cc_final: 0.8002 (tp30) REVERT: E 821 ASP cc_start: 0.8347 (t70) cc_final: 0.7880 (t70) REVERT: E 873 ARG cc_start: 0.8184 (mpp80) cc_final: 0.7898 (mpp80) REVERT: E 918 TYR cc_start: 0.8380 (t80) cc_final: 0.8148 (t80) outliers start: 41 outliers final: 26 residues processed: 238 average time/residue: 0.1690 time to fit residues: 66.2908 Evaluate side-chains 229 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1400 ILE Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 303 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 243 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098353 restraints weight = 35652.763| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.27 r_work: 0.3052 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 27726 Z= 0.259 Angle : 0.602 6.481 38102 Z= 0.302 Chirality : 0.047 0.180 4374 Planarity : 0.004 0.048 4426 Dihedral : 8.293 59.297 4736 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.30 % Allowed : 11.34 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 2972 helix: 1.02 (0.14), residues: 1428 sheet: -0.93 (0.27), residues: 332 loop : -0.13 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 346 TYR 0.025 0.002 TYR A1000 PHE 0.017 0.002 PHE E 362 TRP 0.014 0.002 TRP A 102 HIS 0.007 0.001 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.26 (27726) covalent geometry : angle 0.60164 / 0.30 (38102) hydrogen bonds : bond 0.04764 / 3.26 ( 1247) hydrogen bonds : angle 4.29169 / 3.06 ( 3500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 1.001 Fit side-chains REVERT: A 102 TRP cc_start: 0.8523 (m100) cc_final: 0.8240 (m100) REVERT: A 527 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: A 548 LYS cc_start: 0.8482 (ttpt) cc_final: 0.7893 (tptp) REVERT: A 794 GLU cc_start: 0.8362 (pm20) cc_final: 0.8113 (tp30) REVERT: A 873 ARG cc_start: 0.8304 (mpp80) cc_final: 0.8027 (mpp80) REVERT: A 908 MET cc_start: 0.6191 (mtt) cc_final: 0.5988 (mtt) REVERT: E 102 TRP cc_start: 0.8526 (m100) cc_final: 0.8146 (m100) REVERT: E 527 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: E 548 LYS cc_start: 0.8501 (ttpt) cc_final: 0.7984 (tptp) REVERT: E 552 GLN cc_start: 0.7831 (pp30) cc_final: 0.7354 (pp30) REVERT: E 794 GLU cc_start: 0.8370 (pm20) cc_final: 0.8139 (tp30) REVERT: E 873 ARG cc_start: 0.8308 (mpp80) cc_final: 0.8050 (mpp80) REVERT: E 918 TYR cc_start: 0.8424 (t80) cc_final: 0.8215 (t80) outliers start: 35 outliers final: 26 residues processed: 223 average time/residue: 0.1811 time to fit residues: 65.8588 Evaluate side-chains 221 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1400 ILE Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1400 ILE Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 274 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 5 optimal weight: 0.0070 chunk 94 optimal weight: 0.9990 chunk 294 optimal weight: 5.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.147635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102510 restraints weight = 35301.623| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.03 r_work: 0.3118 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27726 Z= 0.106 Angle : 0.503 6.284 38102 Z= 0.252 Chirality : 0.042 0.166 4374 Planarity : 0.003 0.045 4426 Dihedral : 8.222 59.395 4736 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.89 % Allowed : 12.16 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 2972 helix: 1.20 (0.14), residues: 1456 sheet: -0.83 (0.28), residues: 312 loop : -0.03 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 346 TYR 0.017 0.001 TYR E 740 PHE 0.017 0.001 PHE E 362 TRP 0.012 0.001 TRP A 102 HIS 0.002 0.000 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (27726) covalent geometry : angle 0.50314 / 0.25 (38102) hydrogen bonds : bond 0.03656 / 2.49 ( 1247) hydrogen bonds : angle 3.99832 / 2.85 ( 3500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.993 Fit side-chains REVERT: A 527 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: A 548 LYS cc_start: 0.8446 (ttpt) cc_final: 0.7882 (tptp) REVERT: A 794 GLU cc_start: 0.8275 (pm20) cc_final: 0.8022 (tp30) REVERT: A 821 ASP cc_start: 0.8348 (t70) cc_final: 0.7818 (t0) REVERT: A 873 ARG cc_start: 0.8296 (mpp80) cc_final: 0.8026 (mpp80) REVERT: A 1534 GLU cc_start: 0.7627 (tt0) cc_final: 0.7372 (tt0) REVERT: E 102 TRP cc_start: 0.8450 (m100) cc_final: 0.8126 (m100) REVERT: E 527 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: E 548 LYS cc_start: 0.8470 (ttpt) cc_final: 0.7955 (tptp) REVERT: E 794 GLU cc_start: 0.8304 (pm20) cc_final: 0.8062 (tp30) REVERT: E 821 ASP cc_start: 0.8261 (t70) cc_final: 0.7789 (t70) REVERT: E 873 ARG cc_start: 0.8265 (mpp80) cc_final: 0.7999 (mpp80) outliers start: 24 outliers final: 15 residues processed: 224 average time/residue: 0.1758 time to fit residues: 64.3961 Evaluate side-chains 221 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1504 SER Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1400 ILE Chi-restraints excluded: chain E residue 1504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 2.9990 chunk 157 optimal weight: 50.0000 chunk 272 optimal weight: 0.3980 chunk 175 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 169 optimal weight: 0.0020 chunk 201 optimal weight: 0.8980 chunk 217 optimal weight: 0.0570 overall best weight: 0.4506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.150086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103741 restraints weight = 35572.931| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.41 r_work: 0.3116 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 27726 Z= 0.089 Angle : 0.487 8.806 38102 Z= 0.241 Chirality : 0.042 0.175 4374 Planarity : 0.003 0.043 4426 Dihedral : 8.070 59.189 4736 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.63 % Allowed : 12.49 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2972 helix: 1.41 (0.14), residues: 1452 sheet: -0.81 (0.28), residues: 318 loop : 0.08 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 346 TYR 0.017 0.001 TYR A 740 PHE 0.017 0.001 PHE E1542 TRP 0.013 0.001 TRP A 102 HIS 0.004 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (27726) covalent geometry : angle 0.48690 / 0.24 (38102) hydrogen bonds : bond 0.03210 / 2.19 ( 1247) hydrogen bonds : angle 3.82648 / 2.73 ( 3500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5944 Ramachandran restraints generated. 2972 Oldfield, 0 Emsley, 2972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.018 Fit side-chains REVERT: A 527 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: A 548 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7780 (tptp) REVERT: A 742 GLU cc_start: 0.8729 (tt0) cc_final: 0.8514 (tp30) REVERT: A 794 GLU cc_start: 0.8333 (pm20) cc_final: 0.7966 (tp30) REVERT: A 821 ASP cc_start: 0.8187 (t70) cc_final: 0.7698 (t0) REVERT: A 873 ARG cc_start: 0.8209 (mpp80) cc_final: 0.7899 (mpp80) REVERT: A 1534 GLU cc_start: 0.7565 (tt0) cc_final: 0.7301 (tt0) REVERT: E 527 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: E 548 LYS cc_start: 0.8375 (ttpt) cc_final: 0.7848 (tptp) REVERT: E 742 GLU cc_start: 0.8692 (tt0) cc_final: 0.8480 (tp30) REVERT: E 794 GLU cc_start: 0.8362 (pm20) cc_final: 0.7978 (tp30) REVERT: E 821 ASP cc_start: 0.8244 (t70) cc_final: 0.7699 (t0) REVERT: E 873 ARG cc_start: 0.8214 (mpp80) cc_final: 0.7924 (mpp80) outliers start: 17 outliers final: 15 residues processed: 233 average time/residue: 0.1762 time to fit residues: 67.8398 Evaluate side-chains 220 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASP Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1314 ASP Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 527 ASP Chi-restraints excluded: chain E residue 590 VAL Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 1400 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 208 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101389 restraints weight = 35252.246| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.43 r_work: 0.3091 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27726 Z= 0.108 Angle : 0.498 7.169 38102 Z= 0.248 Chirality : 0.042 0.160 4374 Planarity : 0.003 0.043 4426 Dihedral : 8.084 59.023 4736 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.93 % Allowed : 12.71 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.15), residues: 2972 helix: 1.45 (0.14), residues: 1432 sheet: -0.85 (0.28), residues: 320 loop : 0.11 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 346 TYR 0.016 0.001 TYR E 740 PHE 0.021 0.001 PHE E 362 TRP 0.016 0.001 TRP A 102 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (27726) covalent geometry : angle 0.49831 / 0.25 (38102) hydrogen bonds : bond 0.03487 / 2.38 ( 1247) hydrogen bonds : angle 3.86472 / 2.76 ( 3500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7969.10 seconds wall clock time: 136 minutes 56.67 seconds (8216.67 seconds total)