Starting phenix.real_space_refine on Sun Feb 8 00:08:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr9_40723/02_2026/8sr9_40723.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr9_40723/02_2026/8sr9_40723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sr9_40723/02_2026/8sr9_40723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr9_40723/02_2026/8sr9_40723.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sr9_40723/02_2026/8sr9_40723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr9_40723/02_2026/8sr9_40723.map" } resolution = 3.05 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= 0.140 sd= 1.387 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 Mg 8 5.21 5 S 176 5.16 5 C 24596 2.51 5 N 6684 2.21 5 O 6712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 9458 Classifications: {'peptide': 1352} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 370} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1296} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1323 Unresolved non-hydrogen angles: 1663 Unresolved non-hydrogen dihedrals: 1089 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'ARG:plan': 25, 'GLU:plan': 43, 'ASN:plan1': 21, 'ASP:plan': 54, 'GLN:plan1': 20, 'HIS:plan': 9, 'PHE:plan': 9, 'TYR:plan': 8, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 811 Chain: "D" Number of atoms: 9458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 9458 Classifications: {'peptide': 1352} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 370} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1296} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1323 Unresolved non-hydrogen angles: 1663 Unresolved non-hydrogen dihedrals: 1089 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'ARG:plan': 25, 'GLU:plan': 43, 'ASN:plan1': 21, 'ASP:plan': 54, 'GLN:plan1': 20, 'HIS:plan': 9, 'PHE:plan': 9, 'TYR:plan': 8, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 811 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {' MG': 2, 'CLR': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {' MG': 2, 'CLR': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B, C Time building chain proxies: 14.55, per 1000 atoms: 0.38 Number of scatterers: 38176 At special positions: 0 Unit cell: (152.81, 152.81, 187.502, 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 176 16.00 Mg 8 11.99 O 6712 8.00 N 6684 7.00 C 24596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 376 " distance=0.00 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 399 " distance=0.00 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 446 " distance=0.00 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 609 " distance=0.00 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 676 " distance=0.00 Simple disulfide: pdb=" SG CYS B 817 " - pdb=" SG CYS B 817 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B 997 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B1006 " distance=0.00 Simple disulfide: pdb=" SG CYS B1060 " - pdb=" SG CYS B1060 " distance=0.00 Simple disulfide: pdb=" SG CYS B1439 " - pdb=" SG CYS B1439 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 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: 3.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10176 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 36 sheets defined 60.9% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.572A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.835A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 410 through 421 removed outlier: 3.720A pdb=" N LYS A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.605A pdb=" N ILE A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.829A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.557A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.731A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 3.564A pdb=" N ARG A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 Processing helix chain 'A' and resid 577 through 586 removed outlier: 4.003A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 585 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.599A pdb=" N ARG A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.755A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.666A pdb=" N GLN A 647 " --> pdb=" O ARG A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 651 through 680 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.574A pdb=" N PHE A 695 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 696 " --> pdb=" O ASP A 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 692 through 696' Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.564A pdb=" N VAL A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.670A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 750' Processing helix chain 'A' and resid 788 through 799 removed outlier: 3.922A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 799 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 857 removed outlier: 3.723A pdb=" N CYS A 857 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.953A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.561A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 4.133A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 923 through 961 removed outlier: 3.953A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.646A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1010 through 1012 No H-bonds generated for 'chain 'A' and resid 1010 through 1012' Processing helix chain 'A' and resid 1013 through 1026 Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 5.700A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 3.828A pdb=" N ALA A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1130 Processing helix chain 'A' and resid 1131 through 1167 Processing helix chain 'A' and resid 1235 through 1239 removed outlier: 3.882A pdb=" N VAL A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1403 through 1413 Processing helix chain 'A' and resid 1449 through 1453 removed outlier: 3.624A pdb=" N ARG A1452 " --> pdb=" O HIS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1490 Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.571A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.834A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 410 through 421 removed outlier: 3.720A pdb=" N LYS B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 439 through 457 removed outlier: 3.605A pdb=" N ILE B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.830A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.557A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.731A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 3.565A pdb=" N ARG B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 Processing helix chain 'B' and resid 577 through 586 removed outlier: 4.003A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 582 " --> pdb=" O THR B 579 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.598A pdb=" N ARG B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 642 removed outlier: 3.755A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.666A pdb=" N GLN B 647 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 651 through 680 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.574A pdb=" N PHE B 695 " --> pdb=" O ASN B 692 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 696 " --> pdb=" O ASP B 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.564A pdb=" N VAL B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.669A pdb=" N VAL B 749 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 750' Processing helix chain 'B' and resid 788 through 799 removed outlier: 3.922A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 799 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 857 removed outlier: 3.723A pdb=" N CYS B 857 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 866 removed outlier: 3.953A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.560A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 4.133A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 919 Processing helix chain 'B' and resid 923 through 961 removed outlier: 3.953A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.646A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1010 through 1012 No H-bonds generated for 'chain 'B' and resid 1010 through 1012' Processing helix chain 'B' and resid 1013 through 1026 Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 5.700A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR B1057 " --> pdb=" O ARG B1053 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 3.828A pdb=" N ALA B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1130 Processing helix chain 'B' and resid 1131 through 1167 Processing helix chain 'B' and resid 1235 through 1239 removed outlier: 3.882A pdb=" N VAL B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1378 through 1391 Processing helix chain 'B' and resid 1403 through 1413 Processing helix chain 'B' and resid 1449 through 1453 removed outlier: 3.624A pdb=" N ARG B1452 " --> pdb=" O HIS B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1478 through 1490 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.572A pdb=" N LYS C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 346 through 359 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.834A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 410 through 421 removed outlier: 3.720A pdb=" N LYS C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.606A pdb=" N ILE C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.830A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.557A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.731A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 removed outlier: 3.564A pdb=" N ARG C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 577 through 586 removed outlier: 4.003A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 582 " --> pdb=" O THR C 579 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 585 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.599A pdb=" N ARG C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 642 removed outlier: 3.755A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.666A pdb=" N GLN C 647 " --> pdb=" O ARG C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 651 through 680 Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.574A pdb=" N PHE C 695 " --> pdb=" O ASN C 692 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 696 " --> pdb=" O ASP C 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 692 through 696' Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 removed outlier: 3.564A pdb=" N VAL C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.669A pdb=" N VAL C 749 " --> pdb=" O PHE C 745 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 745 through 750' Processing helix chain 'C' and resid 788 through 799 removed outlier: 3.922A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 799 " --> pdb=" O PHE C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 857 removed outlier: 3.723A pdb=" N CYS C 857 " --> pdb=" O GLN C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.952A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.561A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 4.133A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 919 Processing helix chain 'C' and resid 923 through 961 removed outlier: 3.953A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.646A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1010 through 1012 No H-bonds generated for 'chain 'C' and resid 1010 through 1012' Processing helix chain 'C' and resid 1013 through 1026 Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 5.698A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C1066 " --> pdb=" O GLU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 3.828A pdb=" N ALA C1077 " --> pdb=" O PHE C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1130 Processing helix chain 'C' and resid 1131 through 1167 Processing helix chain 'C' and resid 1235 through 1239 removed outlier: 3.882A pdb=" N VAL C1239 " --> pdb=" O ALA C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1255 through 1260 Processing helix chain 'C' and resid 1378 through 1391 Processing helix chain 'C' and resid 1403 through 1413 Processing helix chain 'C' and resid 1449 through 1453 removed outlier: 3.624A pdb=" N ARG C1452 " --> pdb=" O HIS C1449 " (cutoff:3.500A) Processing helix chain 'C' and resid 1478 through 1490 Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.572A pdb=" N LYS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 323 through 337 Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.834A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 410 through 421 removed outlier: 3.720A pdb=" N LYS D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 439 through 457 removed outlier: 3.604A pdb=" N ILE D 443 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.829A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.557A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.731A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 removed outlier: 3.564A pdb=" N ARG D 553 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 577 through 586 removed outlier: 4.003A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 582 " --> pdb=" O THR D 579 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 585 " --> pdb=" O ASP D 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 586 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.599A pdb=" N ARG D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 642 removed outlier: 3.755A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.666A pdb=" N GLN D 647 " --> pdb=" O ARG D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 651 through 680 Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 692 through 696 removed outlier: 3.574A pdb=" N PHE D 695 " --> pdb=" O ASN D 692 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 696 " --> pdb=" O ASP D 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 692 through 696' Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 removed outlier: 3.564A pdb=" N VAL D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.670A pdb=" N VAL D 749 " --> pdb=" O PHE D 745 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 745 through 750' Processing helix chain 'D' and resid 788 through 799 removed outlier: 3.922A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR D 799 " --> pdb=" O PHE D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 857 removed outlier: 3.723A pdb=" N CYS D 857 " --> pdb=" O GLN D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 866 removed outlier: 3.953A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.561A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 4.133A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 919 Processing helix chain 'D' and resid 923 through 961 removed outlier: 3.953A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.646A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 982 through 984 No H-bonds generated for 'chain 'D' and resid 982 through 984' Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1010 through 1012 No H-bonds generated for 'chain 'D' and resid 1010 through 1012' Processing helix chain 'D' and resid 1013 through 1026 Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 5.700A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D1066 " --> pdb=" O GLU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 3.828A pdb=" N ALA D1077 " --> pdb=" O PHE D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 Processing helix chain 'D' and resid 1131 through 1167 Processing helix chain 'D' and resid 1235 through 1239 removed outlier: 3.882A pdb=" N VAL D1239 " --> pdb=" O ALA D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1378 through 1391 Processing helix chain 'D' and resid 1403 through 1413 Processing helix chain 'D' and resid 1449 through 1453 removed outlier: 3.625A pdb=" N ARG D1452 " --> pdb=" O HIS D1449 " (cutoff:3.500A) Processing helix chain 'D' and resid 1478 through 1490 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.480A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1251 through 1252 removed outlier: 6.330A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA6, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 4.014A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.224A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 14.127A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 18.165A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY A1324 " --> pdb=" O TRP A1434 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU A1436 " --> pdb=" O GLY A1324 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASN A1326 " --> pdb=" O GLU A1436 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR A1438 " --> pdb=" O ASN A1326 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A1328 " --> pdb=" O THR A1438 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL A1440 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP A1330 " --> pdb=" O VAL A1440 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE A1442 " --> pdb=" O ASP A1330 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A1332 " --> pdb=" O PHE A1442 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP A1444 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A1334 " --> pdb=" O ASP A1444 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A1420 " --> pdb=" O CYS A1439 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN A1441 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE A1418 " --> pdb=" O ASN A1441 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS A1443 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY A1416 " --> pdb=" O HIS A1443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 18.165A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 14.127A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU A1353 " --> pdb=" O MET A1468 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET A1468 " --> pdb=" O LEU A1353 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE A1355 " --> pdb=" O TRP A1466 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP A1466 " --> pdb=" O PHE A1355 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A1357 " --> pdb=" O ALA A1464 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA A1464 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A1359 " --> pdb=" O GLU A1462 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 236 removed outlier: 6.480A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1251 through 1252 removed outlier: 6.330A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AB6, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 4.014A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.223A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 14.126A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 18.166A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY B1324 " --> pdb=" O TRP B1434 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU B1436 " --> pdb=" O GLY B1324 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASN B1326 " --> pdb=" O GLU B1436 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR B1438 " --> pdb=" O ASN B1326 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B1328 " --> pdb=" O THR B1438 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL B1440 " --> pdb=" O ALA B1328 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP B1330 " --> pdb=" O VAL B1440 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE B1442 " --> pdb=" O ASP B1330 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B1332 " --> pdb=" O PHE B1442 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP B1444 " --> pdb=" O VAL B1332 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B1334 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1370 through 1372 removed outlier: 18.166A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 14.126A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B1353 " --> pdb=" O MET B1468 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET B1468 " --> pdb=" O LEU B1353 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE B1355 " --> pdb=" O TRP B1466 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP B1466 " --> pdb=" O PHE B1355 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B1357 " --> pdb=" O ALA B1464 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA B1464 " --> pdb=" O ALA B1357 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN B1359 " --> pdb=" O GLU B1462 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AC1, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AC2, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AC3, first strand: chain 'C' and resid 232 through 236 removed outlier: 6.479A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 6.331A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AC6, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 4.014A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.224A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 14.126A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 18.166A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY C1324 " --> pdb=" O TRP C1434 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU C1436 " --> pdb=" O GLY C1324 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASN C1326 " --> pdb=" O GLU C1436 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR C1438 " --> pdb=" O ASN C1326 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C1328 " --> pdb=" O THR C1438 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL C1440 " --> pdb=" O ALA C1328 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP C1330 " --> pdb=" O VAL C1440 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE C1442 " --> pdb=" O ASP C1330 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C1332 " --> pdb=" O PHE C1442 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP C1444 " --> pdb=" O VAL C1332 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR C1334 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1370 through 1372 removed outlier: 18.166A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 14.126A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU C1353 " --> pdb=" O MET C1468 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET C1468 " --> pdb=" O LEU C1353 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE C1355 " --> pdb=" O TRP C1466 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP C1466 " --> pdb=" O PHE C1355 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C1357 " --> pdb=" O ALA C1464 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA C1464 " --> pdb=" O ALA C1357 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C1359 " --> pdb=" O GLU C1462 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD1, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AD2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD3, first strand: chain 'D' and resid 232 through 236 removed outlier: 6.480A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1251 through 1252 removed outlier: 6.331A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AD6, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 4.015A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.223A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 14.126A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 18.166A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY D1324 " --> pdb=" O TRP D1434 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU D1436 " --> pdb=" O GLY D1324 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASN D1326 " --> pdb=" O GLU D1436 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR D1438 " --> pdb=" O ASN D1326 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA D1328 " --> pdb=" O THR D1438 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL D1440 " --> pdb=" O ALA D1328 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP D1330 " --> pdb=" O VAL D1440 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE D1442 " --> pdb=" O ASP D1330 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL D1332 " --> pdb=" O PHE D1442 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP D1444 " --> pdb=" O VAL D1332 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR D1334 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1370 through 1372 removed outlier: 18.166A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 14.126A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU D1353 " --> pdb=" O MET D1468 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET D1468 " --> pdb=" O LEU D1353 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE D1355 " --> pdb=" O TRP D1466 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP D1466 " --> pdb=" O PHE D1355 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA D1357 " --> pdb=" O ALA D1464 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA D1464 " --> pdb=" O ALA D1357 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN D1359 " --> pdb=" O GLU D1462 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1346 through 1347 2344 hydrogen bonds defined for protein. 6864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.98 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6232 1.32 - 1.44: 10340 1.44 - 1.57: 22132 1.57 - 1.70: 4 1.70 - 1.83: 312 Bond restraints: 39020 Sorted by residual: bond pdb=" C PRO B 978 " pdb=" O PRO B 978 " ideal model delta sigma weight residual 1.238 1.189 0.048 1.24e-02 6.50e+03 1.51e+01 bond pdb=" C PRO C 978 " pdb=" O PRO C 978 " ideal model delta sigma weight residual 1.238 1.189 0.048 1.24e-02 6.50e+03 1.51e+01 bond pdb=" C PRO A 978 " pdb=" O PRO A 978 " ideal model delta sigma weight residual 1.238 1.189 0.048 1.24e-02 6.50e+03 1.51e+01 bond pdb=" C PRO D 978 " pdb=" O PRO D 978 " ideal model delta sigma weight residual 1.238 1.189 0.048 1.24e-02 6.50e+03 1.51e+01 bond pdb=" C PRO B1015 " pdb=" O PRO B1015 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.20e-02 6.94e+03 1.50e+01 ... (remaining 39015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 48486 2.65 - 5.30: 4370 5.30 - 7.95: 448 7.95 - 10.60: 64 10.60 - 13.25: 4 Bond angle restraints: 53372 Sorted by residual: angle pdb=" C GLN D 408 " pdb=" N GLY D 409 " pdb=" CA GLY D 409 " ideal model delta sigma weight residual 120.00 127.30 -7.30 1.10e+00 8.26e-01 4.41e+01 angle pdb=" C GLN C 408 " pdb=" N GLY C 409 " pdb=" CA GLY C 409 " ideal model delta sigma weight residual 120.00 127.30 -7.30 1.10e+00 8.26e-01 4.41e+01 angle pdb=" C GLN A 408 " pdb=" N GLY A 409 " pdb=" CA GLY A 409 " ideal model delta sigma weight residual 120.00 127.30 -7.30 1.10e+00 8.26e-01 4.41e+01 angle pdb=" C GLN B 408 " pdb=" N GLY B 409 " pdb=" CA GLY B 409 " ideal model delta sigma weight residual 120.00 127.27 -7.27 1.10e+00 8.26e-01 4.36e+01 angle pdb=" N VAL C 844 " pdb=" CA VAL C 844 " pdb=" C VAL C 844 " ideal model delta sigma weight residual 110.53 104.48 6.05 9.40e-01 1.13e+00 4.15e+01 ... (remaining 53367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 21824 17.52 - 35.04: 1397 35.04 - 52.57: 212 52.57 - 70.09: 32 70.09 - 87.61: 36 Dihedral angle restraints: 23501 sinusoidal: 7813 harmonic: 15688 Sorted by residual: dihedral pdb=" C THR D 877 " pdb=" N THR D 877 " pdb=" CA THR D 877 " pdb=" CB THR D 877 " ideal model delta harmonic sigma weight residual -122.00 -132.12 10.12 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" C THR B 877 " pdb=" N THR B 877 " pdb=" CA THR B 877 " pdb=" CB THR B 877 " ideal model delta harmonic sigma weight residual -122.00 -132.09 10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" C THR A 877 " pdb=" N THR A 877 " pdb=" CA THR A 877 " pdb=" CB THR A 877 " ideal model delta harmonic sigma weight residual -122.00 -132.09 10.09 0 2.50e+00 1.60e-01 1.63e+01 ... (remaining 23498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5301 0.110 - 0.221: 899 0.221 - 0.331: 96 0.331 - 0.441: 17 0.441 - 0.552: 11 Chirality restraints: 6324 Sorted by residual: chirality pdb=" CB VAL A 519 " pdb=" CA VAL A 519 " pdb=" CG1 VAL A 519 " pdb=" CG2 VAL A 519 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" CB VAL D 519 " pdb=" CA VAL D 519 " pdb=" CG1 VAL D 519 " pdb=" CG2 VAL D 519 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" CB VAL C 519 " pdb=" CA VAL C 519 " pdb=" CG1 VAL C 519 " pdb=" CG2 VAL C 519 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.57e+00 ... (remaining 6321 not shown) Planarity restraints: 6868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 651 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C LEU C 651 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU C 651 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA C 652 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 651 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C LEU A 651 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU A 651 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA A 652 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 651 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C LEU D 651 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 651 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA D 652 " -0.023 2.00e-02 2.50e+03 ... (remaining 6865 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 117 2.54 - 3.13: 24817 3.13 - 3.72: 59303 3.72 - 4.31: 76911 4.31 - 4.90: 132482 Nonbonded interactions: 293630 Sorted by model distance: nonbonded pdb=" O LEU D 621 " pdb="MG MG D6004 " model vdw 1.948 2.170 nonbonded pdb=" O LEU A 621 " pdb="MG MG A3002 " model vdw 1.948 2.170 nonbonded pdb=" O LEU B 621 " pdb="MG MG B3002 " model vdw 1.948 2.170 nonbonded pdb=" O LEU C 621 " pdb="MG MG C3002 " model vdw 1.948 2.170 nonbonded pdb=" SG CYS D 997 " pdb=" SG CYS D1006 " model vdw 2.031 3.760 ... (remaining 293625 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: 0.12 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 1494 or resid 3005)) selection = (chain 'B' and (resid 46 through 1494 or resid 3005)) selection = (chain 'C' and (resid 46 through 1494 or resid 3005)) selection = (chain 'D' and (resid 46 through 1494 or resid 6005)) } 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 43.530 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.060 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 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 : 0.010 0.079 39023 Z= 0.623 Angle : 1.553 13.248 53388 Z= 1.041 Chirality : 0.083 0.552 6324 Planarity : 0.010 0.038 6868 Dihedral : 12.150 87.609 13296 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.51 % Allowed : 1.78 % Favored : 97.71 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.82 % 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: 0.16 (0.11), residues: 5368 helix: 0.51 (0.09), residues: 2960 sheet: -0.97 (0.23), residues: 404 loop : -0.04 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 517 TYR 0.036 0.005 TYR B 504 PHE 0.049 0.004 PHE B 941 TRP 0.035 0.004 TRP D1052 HIS 0.033 0.004 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.01036 (39020) covalent geometry : angle 1.55360 (53372) SS BOND : bond 0.00051 ( 3) SS BOND : angle 0.71000 ( 16) hydrogen bonds : bond 0.16899 ( 2332) hydrogen bonds : angle 7.50078 ( 6864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 754 time to evaluate : 1.374 Fit side-chains REVERT: A 50 GLN cc_start: 0.3218 (pm20) cc_final: 0.2314 (tp40) REVERT: A 280 ASN cc_start: 0.5947 (m-40) cc_final: 0.5381 (m110) REVERT: A 284 GLN cc_start: 0.6969 (mm110) cc_final: 0.6683 (mm110) REVERT: A 452 MET cc_start: 0.6604 (tpt) cc_final: 0.6191 (tpt) REVERT: A 474 TYR cc_start: 0.7474 (p90) cc_final: 0.7097 (p90) REVERT: A 502 GLU cc_start: 0.5801 (mt-10) cc_final: 0.5368 (mm-30) REVERT: A 585 TYR cc_start: 0.5547 (m-80) cc_final: 0.5043 (m-80) REVERT: A 622 ILE cc_start: 0.8154 (mt) cc_final: 0.7925 (mm) REVERT: A 660 HIS cc_start: 0.5823 (t70) cc_final: 0.5257 (t70) REVERT: A 694 MET cc_start: 0.6008 (ttm) cc_final: 0.5570 (ttp) REVERT: A 741 PHE cc_start: 0.6265 (t80) cc_final: 0.6007 (t80) REVERT: A 745 PHE cc_start: 0.5903 (m-80) cc_final: 0.5639 (m-80) REVERT: A 811 LEU cc_start: 0.7408 (mt) cc_final: 0.7146 (mt) REVERT: A 856 PHE cc_start: 0.6239 (m-80) cc_final: 0.5395 (m-80) REVERT: A 875 MET cc_start: 0.6119 (ptt) cc_final: 0.5761 (ptm) REVERT: A 923 ASN cc_start: 0.6939 (t0) cc_final: 0.6618 (m-40) REVERT: A 931 MET cc_start: 0.6110 (mtp) cc_final: 0.5779 (mtp) REVERT: A 933 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6273 (tp30) REVERT: A 935 MET cc_start: 0.6555 (mmm) cc_final: 0.6251 (mmt) REVERT: A 965 ASP cc_start: 0.8074 (m-30) cc_final: 0.7793 (m-30) REVERT: A 1004 THR cc_start: 0.7706 (m) cc_final: 0.7407 (p) REVERT: A 1005 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6833 (mt-10) REVERT: A 1051 LEU cc_start: 0.6733 (tp) cc_final: 0.5948 (mp) REVERT: A 1084 MET cc_start: 0.4805 (mmp) cc_final: 0.4598 (mmp) REVERT: A 1085 ARG cc_start: 0.4717 (ttm170) cc_final: 0.3372 (ttm170) REVERT: A 1106 LYS cc_start: 0.5635 (ttmm) cc_final: 0.5206 (mttt) REVERT: A 1114 GLU cc_start: 0.5294 (tp30) cc_final: 0.4888 (mm-30) REVERT: A 1131 MET cc_start: 0.6221 (mtm) cc_final: 0.6001 (mtm) REVERT: A 1138 MET cc_start: 0.6936 (tmm) cc_final: 0.6585 (tmm) REVERT: A 1140 ASN cc_start: 0.6797 (t0) cc_final: 0.6541 (t0) REVERT: A 1147 MET cc_start: 0.6134 (mtp) cc_final: 0.5931 (mtp) REVERT: A 1157 MET cc_start: 0.5976 (ttt) cc_final: 0.5719 (tmm) REVERT: A 1158 ILE cc_start: 0.6593 (mm) cc_final: 0.6361 (mm) REVERT: B 50 GLN cc_start: 0.3242 (pm20) cc_final: 0.2315 (tp-100) REVERT: B 280 ASN cc_start: 0.5952 (m-40) cc_final: 0.5383 (m110) REVERT: B 284 GLN cc_start: 0.6959 (mm110) cc_final: 0.6675 (mm110) REVERT: B 452 MET cc_start: 0.6588 (tpt) cc_final: 0.6187 (tpt) REVERT: B 474 TYR cc_start: 0.7473 (p90) cc_final: 0.7088 (p90) REVERT: B 502 GLU cc_start: 0.5775 (mt-10) cc_final: 0.5352 (mm-30) REVERT: B 530 HIS cc_start: 0.6026 (t70) cc_final: 0.5767 (t70) REVERT: B 585 TYR cc_start: 0.5568 (m-80) cc_final: 0.5028 (m-80) REVERT: B 622 ILE cc_start: 0.8156 (mt) cc_final: 0.7926 (mm) REVERT: B 660 HIS cc_start: 0.5830 (t70) cc_final: 0.5268 (t70) REVERT: B 694 MET cc_start: 0.6002 (ttm) cc_final: 0.5569 (ttp) REVERT: B 741 PHE cc_start: 0.6259 (t80) cc_final: 0.6000 (t80) REVERT: B 745 PHE cc_start: 0.5891 (m-80) cc_final: 0.5626 (m-80) REVERT: B 811 LEU cc_start: 0.7407 (mt) cc_final: 0.7145 (mt) REVERT: B 856 PHE cc_start: 0.6237 (m-80) cc_final: 0.5392 (m-80) REVERT: B 875 MET cc_start: 0.6116 (ptt) cc_final: 0.5752 (ptm) REVERT: B 923 ASN cc_start: 0.6936 (t0) cc_final: 0.6622 (m-40) REVERT: B 931 MET cc_start: 0.6093 (mtp) cc_final: 0.5744 (mtp) REVERT: B 933 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6276 (tp30) REVERT: B 935 MET cc_start: 0.6572 (mmm) cc_final: 0.6278 (mmt) REVERT: B 965 ASP cc_start: 0.8090 (m-30) cc_final: 0.7800 (m-30) REVERT: B 1004 THR cc_start: 0.7715 (m) cc_final: 0.7411 (p) REVERT: B 1005 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6801 (mt-10) REVERT: B 1051 LEU cc_start: 0.6680 (tp) cc_final: 0.5912 (mp) REVERT: B 1084 MET cc_start: 0.4806 (mmp) cc_final: 0.4597 (mmp) REVERT: B 1085 ARG cc_start: 0.4680 (ttm170) cc_final: 0.3354 (ttm170) REVERT: B 1106 LYS cc_start: 0.5636 (ttmm) cc_final: 0.5209 (mttt) REVERT: B 1114 GLU cc_start: 0.5285 (tp30) cc_final: 0.4890 (mm-30) REVERT: B 1131 MET cc_start: 0.6244 (mtm) cc_final: 0.6023 (mtm) REVERT: B 1138 MET cc_start: 0.6949 (tmm) cc_final: 0.6542 (tmm) REVERT: B 1140 ASN cc_start: 0.6827 (t0) cc_final: 0.6569 (t0) REVERT: B 1147 MET cc_start: 0.6106 (mtp) cc_final: 0.5904 (mtp) REVERT: B 1157 MET cc_start: 0.5952 (ttt) cc_final: 0.5708 (tmm) REVERT: B 1158 ILE cc_start: 0.6597 (mm) cc_final: 0.6366 (mm) REVERT: C 50 GLN cc_start: 0.3236 (pm20) cc_final: 0.2316 (tp-100) REVERT: C 280 ASN cc_start: 0.5951 (m-40) cc_final: 0.5383 (m110) REVERT: C 284 GLN cc_start: 0.6961 (mm110) cc_final: 0.6676 (mm110) REVERT: C 452 MET cc_start: 0.6609 (tpt) cc_final: 0.6200 (tpt) REVERT: C 474 TYR cc_start: 0.7476 (p90) cc_final: 0.7095 (p90) REVERT: C 502 GLU cc_start: 0.5769 (mt-10) cc_final: 0.5347 (mm-30) REVERT: C 530 HIS cc_start: 0.6022 (t70) cc_final: 0.5767 (t70) REVERT: C 585 TYR cc_start: 0.5586 (m-80) cc_final: 0.5037 (m-80) REVERT: C 622 ILE cc_start: 0.8157 (mt) cc_final: 0.7928 (mm) REVERT: C 660 HIS cc_start: 0.5822 (t70) cc_final: 0.5258 (t70) REVERT: C 694 MET cc_start: 0.6011 (ttm) cc_final: 0.5573 (ttp) REVERT: C 741 PHE cc_start: 0.6261 (t80) cc_final: 0.6002 (t80) REVERT: C 745 PHE cc_start: 0.5891 (m-80) cc_final: 0.5626 (m-80) REVERT: C 811 LEU cc_start: 0.7394 (mt) cc_final: 0.7131 (mt) REVERT: C 856 PHE cc_start: 0.6237 (m-80) cc_final: 0.5393 (m-80) REVERT: C 875 MET cc_start: 0.6123 (ptt) cc_final: 0.5764 (ptm) REVERT: C 923 ASN cc_start: 0.6944 (t0) cc_final: 0.6622 (m-40) REVERT: C 931 MET cc_start: 0.6106 (mtp) cc_final: 0.5799 (mtp) REVERT: C 933 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6297 (tp30) REVERT: C 935 MET cc_start: 0.6568 (mmm) cc_final: 0.6250 (mmt) REVERT: C 965 ASP cc_start: 0.8091 (m-30) cc_final: 0.7815 (m-30) REVERT: C 1004 THR cc_start: 0.7716 (m) cc_final: 0.7413 (p) REVERT: C 1005 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6801 (mt-10) REVERT: C 1051 LEU cc_start: 0.6699 (tp) cc_final: 0.5941 (mp) REVERT: C 1084 MET cc_start: 0.4813 (mmp) cc_final: 0.4605 (mmp) REVERT: C 1085 ARG cc_start: 0.4718 (ttm170) cc_final: 0.3376 (ttm170) REVERT: C 1106 LYS cc_start: 0.5638 (ttmm) cc_final: 0.5209 (mttt) REVERT: C 1114 GLU cc_start: 0.5288 (tp30) cc_final: 0.4890 (mm-30) REVERT: C 1131 MET cc_start: 0.6242 (mtm) cc_final: 0.6022 (mtm) REVERT: C 1138 MET cc_start: 0.6944 (tmm) cc_final: 0.6491 (tmm) REVERT: C 1140 ASN cc_start: 0.6808 (t0) cc_final: 0.6543 (t0) REVERT: C 1147 MET cc_start: 0.6140 (mtp) cc_final: 0.5939 (mtp) REVERT: C 1157 MET cc_start: 0.6001 (ttt) cc_final: 0.5740 (tmm) REVERT: C 1158 ILE cc_start: 0.6593 (mm) cc_final: 0.6365 (mm) REVERT: D 50 GLN cc_start: 0.3236 (pm20) cc_final: 0.2314 (tp-100) REVERT: D 280 ASN cc_start: 0.5953 (m-40) cc_final: 0.5384 (m110) REVERT: D 284 GLN cc_start: 0.6960 (mm110) cc_final: 0.6677 (mm110) REVERT: D 452 MET cc_start: 0.6608 (tpt) cc_final: 0.6204 (tpt) REVERT: D 474 TYR cc_start: 0.7478 (p90) cc_final: 0.7097 (p90) REVERT: D 502 GLU cc_start: 0.5765 (mt-10) cc_final: 0.5343 (mm-30) REVERT: D 530 HIS cc_start: 0.6044 (t70) cc_final: 0.5790 (t70) REVERT: D 585 TYR cc_start: 0.5583 (m-80) cc_final: 0.5039 (m-80) REVERT: D 622 ILE cc_start: 0.8156 (mt) cc_final: 0.7929 (mm) REVERT: D 660 HIS cc_start: 0.5832 (t70) cc_final: 0.5269 (t70) REVERT: D 694 MET cc_start: 0.6012 (ttm) cc_final: 0.5570 (ttp) REVERT: D 741 PHE cc_start: 0.6262 (t80) cc_final: 0.6002 (t80) REVERT: D 745 PHE cc_start: 0.5890 (m-80) cc_final: 0.5624 (m-80) REVERT: D 811 LEU cc_start: 0.7393 (mt) cc_final: 0.7131 (mt) REVERT: D 856 PHE cc_start: 0.6238 (m-80) cc_final: 0.5390 (m-80) REVERT: D 875 MET cc_start: 0.6124 (ptt) cc_final: 0.5765 (ptm) REVERT: D 923 ASN cc_start: 0.6942 (t0) cc_final: 0.6624 (m-40) REVERT: D 931 MET cc_start: 0.6105 (mtp) cc_final: 0.5797 (mtp) REVERT: D 933 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6266 (tp30) REVERT: D 935 MET cc_start: 0.6565 (mmm) cc_final: 0.6250 (mmt) REVERT: D 965 ASP cc_start: 0.8089 (m-30) cc_final: 0.7814 (m-30) REVERT: D 1004 THR cc_start: 0.7715 (m) cc_final: 0.7412 (p) REVERT: D 1005 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6802 (mt-10) REVERT: D 1051 LEU cc_start: 0.6700 (tp) cc_final: 0.5944 (mp) REVERT: D 1084 MET cc_start: 0.4815 (mmp) cc_final: 0.4608 (mmp) REVERT: D 1085 ARG cc_start: 0.4729 (ttm170) cc_final: 0.3380 (ttm170) REVERT: D 1106 LYS cc_start: 0.5639 (ttmm) cc_final: 0.5211 (mttt) REVERT: D 1114 GLU cc_start: 0.5312 (tp30) cc_final: 0.4915 (mm-30) REVERT: D 1131 MET cc_start: 0.6245 (mtm) cc_final: 0.6024 (mtm) REVERT: D 1138 MET cc_start: 0.6944 (tmm) cc_final: 0.6493 (tmm) REVERT: D 1140 ASN cc_start: 0.6813 (t0) cc_final: 0.6483 (t0) REVERT: D 1157 MET cc_start: 0.5998 (ttt) cc_final: 0.5722 (tmm) REVERT: D 1158 ILE cc_start: 0.6593 (mm) cc_final: 0.6362 (mm) outliers start: 16 outliers final: 8 residues processed: 770 average time/residue: 0.2626 time to fit residues: 320.5123 Evaluate side-chains 466 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 458 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 1087 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 30.0000 chunk 497 optimal weight: 0.0570 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 0.5980 chunk 366 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 HIS A 813 HIS B 255 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 HIS B 813 HIS B1152 GLN C 255 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 HIS C 813 HIS C1152 GLN D 255 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 689 HIS D 813 HIS D1152 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.175518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.136985 restraints weight = 57562.201| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.86 r_work: 0.3503 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 39023 Z= 0.118 Angle : 0.495 5.799 53388 Z= 0.266 Chirality : 0.038 0.130 6324 Planarity : 0.004 0.049 6868 Dihedral : 5.381 88.780 6504 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.30 % Allowed : 6.87 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.68 (0.11), residues: 5368 helix: 2.02 (0.09), residues: 2996 sheet: -0.66 (0.24), residues: 388 loop : 0.18 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 916 TYR 0.014 0.001 TYR A 332 PHE 0.012 0.001 PHE A 278 TRP 0.015 0.001 TRP B1052 HIS 0.004 0.001 HIS B 601 Details of bonding type rmsd covalent geometry : bond 0.00242 (39020) covalent geometry : angle 0.49491 (53372) SS BOND : bond 0.00038 ( 3) SS BOND : angle 0.03428 ( 16) hydrogen bonds : bond 0.04392 ( 2332) hydrogen bonds : angle 4.09939 ( 6864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 534 time to evaluate : 1.454 Fit side-chains REVERT: A 50 GLN cc_start: 0.3226 (pm20) cc_final: 0.2290 (tp-100) REVERT: A 280 ASN cc_start: 0.6356 (m-40) cc_final: 0.5717 (m110) REVERT: A 345 TYR cc_start: 0.7172 (m-80) cc_final: 0.6806 (m-80) REVERT: A 474 TYR cc_start: 0.8202 (p90) cc_final: 0.7460 (p90) REVERT: A 502 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6817 (mm-30) REVERT: A 585 TYR cc_start: 0.5707 (m-80) cc_final: 0.5274 (m-80) REVERT: A 690 SER cc_start: 0.7619 (p) cc_final: 0.7407 (p) REVERT: A 745 PHE cc_start: 0.6820 (m-80) cc_final: 0.6316 (m-80) REVERT: A 856 PHE cc_start: 0.6936 (m-80) cc_final: 0.6242 (m-80) REVERT: A 875 MET cc_start: 0.7634 (ptt) cc_final: 0.7229 (ptm) REVERT: A 1005 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 1051 LEU cc_start: 0.8296 (tp) cc_final: 0.7879 (mp) REVERT: A 1085 ARG cc_start: 0.5535 (ttm170) cc_final: 0.4009 (mtt90) REVERT: A 1106 LYS cc_start: 0.6720 (ttmm) cc_final: 0.6176 (mttt) REVERT: A 1114 GLU cc_start: 0.6721 (tp30) cc_final: 0.6506 (mm-30) REVERT: A 1130 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6369 (mp0) REVERT: A 1140 ASN cc_start: 0.7743 (t0) cc_final: 0.7503 (t0) REVERT: A 1147 MET cc_start: 0.6642 (mtp) cc_final: 0.6288 (mtp) REVERT: A 1149 MET cc_start: 0.6820 (ttm) cc_final: 0.6615 (ttm) REVERT: A 1157 MET cc_start: 0.6002 (ttt) cc_final: 0.5551 (tmm) REVERT: A 1467 MET cc_start: 0.4890 (ptm) cc_final: 0.4384 (ptp) REVERT: B 50 GLN cc_start: 0.3136 (pm20) cc_final: 0.2208 (tp-100) REVERT: B 280 ASN cc_start: 0.6335 (m-40) cc_final: 0.5648 (m110) REVERT: B 345 TYR cc_start: 0.7182 (m-80) cc_final: 0.6814 (m-80) REVERT: B 502 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6904 (mm-30) REVERT: B 585 TYR cc_start: 0.5709 (m-80) cc_final: 0.5285 (m-80) REVERT: B 745 PHE cc_start: 0.6824 (m-80) cc_final: 0.6323 (m-80) REVERT: B 856 PHE cc_start: 0.6927 (m-80) cc_final: 0.6234 (m-80) REVERT: B 875 MET cc_start: 0.7635 (ptt) cc_final: 0.7234 (ptm) REVERT: B 1005 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7591 (mt-10) REVERT: B 1051 LEU cc_start: 0.8286 (tp) cc_final: 0.7867 (mp) REVERT: B 1085 ARG cc_start: 0.5514 (ttm170) cc_final: 0.3998 (mtt90) REVERT: B 1106 LYS cc_start: 0.6694 (ttmm) cc_final: 0.6157 (mttt) REVERT: B 1130 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: B 1140 ASN cc_start: 0.7744 (t0) cc_final: 0.7510 (t0) REVERT: B 1147 MET cc_start: 0.6693 (mtp) cc_final: 0.6368 (mtp) REVERT: B 1149 MET cc_start: 0.6851 (ttm) cc_final: 0.6600 (ttm) REVERT: B 1157 MET cc_start: 0.6020 (ttt) cc_final: 0.5672 (tmm) REVERT: B 1467 MET cc_start: 0.4887 (ptm) cc_final: 0.4383 (ptp) REVERT: C 50 GLN cc_start: 0.3238 (pm20) cc_final: 0.2288 (tp-100) REVERT: C 280 ASN cc_start: 0.6361 (m-40) cc_final: 0.5684 (m110) REVERT: C 345 TYR cc_start: 0.7178 (m-80) cc_final: 0.6824 (m-80) REVERT: C 502 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6882 (mm-30) REVERT: C 585 TYR cc_start: 0.5712 (m-80) cc_final: 0.5277 (m-80) REVERT: C 690 SER cc_start: 0.7602 (p) cc_final: 0.7387 (p) REVERT: C 745 PHE cc_start: 0.6817 (m-80) cc_final: 0.6305 (m-80) REVERT: C 856 PHE cc_start: 0.6928 (m-80) cc_final: 0.6233 (m-80) REVERT: C 875 MET cc_start: 0.7627 (ptt) cc_final: 0.7239 (ptm) REVERT: C 1005 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7560 (mt-10) REVERT: C 1051 LEU cc_start: 0.8290 (tp) cc_final: 0.7873 (mp) REVERT: C 1085 ARG cc_start: 0.5501 (ttm170) cc_final: 0.3994 (mtt90) REVERT: C 1106 LYS cc_start: 0.6725 (ttmm) cc_final: 0.6185 (mttt) REVERT: C 1114 GLU cc_start: 0.6692 (tp30) cc_final: 0.6485 (mm-30) REVERT: C 1130 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: C 1140 ASN cc_start: 0.7729 (t0) cc_final: 0.7492 (t0) REVERT: C 1147 MET cc_start: 0.6656 (mtp) cc_final: 0.6304 (mtp) REVERT: C 1149 MET cc_start: 0.6888 (ttm) cc_final: 0.6667 (ttm) REVERT: C 1157 MET cc_start: 0.6090 (ttt) cc_final: 0.5721 (tmm) REVERT: C 1467 MET cc_start: 0.4898 (ptm) cc_final: 0.4403 (ptp) REVERT: D 50 GLN cc_start: 0.3256 (pm20) cc_final: 0.2311 (tp-100) REVERT: D 220 ILE cc_start: 0.6458 (mt) cc_final: 0.6256 (pt) REVERT: D 280 ASN cc_start: 0.6358 (m-40) cc_final: 0.5708 (m110) REVERT: D 345 TYR cc_start: 0.7181 (m-80) cc_final: 0.6820 (m-80) REVERT: D 502 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6877 (mm-30) REVERT: D 585 TYR cc_start: 0.5706 (m-80) cc_final: 0.5280 (m-80) REVERT: D 690 SER cc_start: 0.7607 (p) cc_final: 0.7387 (p) REVERT: D 745 PHE cc_start: 0.6820 (m-80) cc_final: 0.6310 (m-80) REVERT: D 856 PHE cc_start: 0.6923 (m-80) cc_final: 0.6230 (m-80) REVERT: D 875 MET cc_start: 0.7633 (ptt) cc_final: 0.7242 (ptm) REVERT: D 1005 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7516 (mt-10) REVERT: D 1051 LEU cc_start: 0.8297 (tp) cc_final: 0.7875 (mp) REVERT: D 1085 ARG cc_start: 0.5489 (ttm170) cc_final: 0.3978 (mtt90) REVERT: D 1106 LYS cc_start: 0.6715 (ttmm) cc_final: 0.6157 (mttt) REVERT: D 1130 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: D 1140 ASN cc_start: 0.7742 (t0) cc_final: 0.7450 (t0) REVERT: D 1147 MET cc_start: 0.6782 (mtm) cc_final: 0.6573 (mtp) REVERT: D 1149 MET cc_start: 0.6847 (ttm) cc_final: 0.6494 (ttm) REVERT: D 1157 MET cc_start: 0.6124 (ttt) cc_final: 0.5746 (tmm) REVERT: D 1467 MET cc_start: 0.4894 (ptm) cc_final: 0.4397 (ptp) outliers start: 41 outliers final: 12 residues processed: 554 average time/residue: 0.2393 time to fit residues: 217.4074 Evaluate side-chains 438 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 422 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1130 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 83 optimal weight: 3.9990 chunk 526 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 375 optimal weight: 4.9990 chunk 516 optimal weight: 5.9990 chunk 420 optimal weight: 1.9990 chunk 416 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 204 optimal weight: 8.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 413 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS A 660 HIS ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 ASN A1145 GLN A1156 HIS B 254 HIS B 413 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 HIS B 660 HIS B1140 ASN B1145 GLN C 254 HIS C 413 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 HIS C 660 HIS C1140 ASN C1145 GLN D 254 HIS D 413 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 HIS D 660 HIS ** D1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1145 GLN D1156 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.172731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.140932 restraints weight = 57124.619| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.04 r_work: 0.3487 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 39023 Z= 0.214 Angle : 0.647 6.822 53388 Z= 0.339 Chirality : 0.043 0.161 6324 Planarity : 0.005 0.058 6868 Dihedral : 6.112 81.265 6500 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.80 % Allowed : 9.64 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.98 (0.11), residues: 5368 helix: 1.46 (0.09), residues: 3000 sheet: -1.23 (0.22), residues: 416 loop : -0.05 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 594 TYR 0.035 0.003 TYR A 863 PHE 0.026 0.002 PHE C 880 TRP 0.015 0.002 TRP D 620 HIS 0.009 0.002 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00499 (39020) covalent geometry : angle 0.64712 (53372) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.16974 ( 16) hydrogen bonds : bond 0.05235 ( 2332) hydrogen bonds : angle 4.40504 ( 6864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 428 time to evaluate : 1.375 Fit side-chains REVERT: A 232 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.6057 (mmtt) REVERT: A 279 GLU cc_start: 0.6317 (mt-10) cc_final: 0.6017 (mt-10) REVERT: A 413 ASN cc_start: 0.6755 (m-40) cc_final: 0.6554 (t0) REVERT: A 585 TYR cc_start: 0.6102 (m-80) cc_final: 0.5820 (m-80) REVERT: A 745 PHE cc_start: 0.6846 (m-80) cc_final: 0.6534 (m-80) REVERT: A 1051 LEU cc_start: 0.8256 (tp) cc_final: 0.7811 (mp) REVERT: A 1082 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6389 (tp) REVERT: A 1083 PHE cc_start: 0.6268 (t80) cc_final: 0.6043 (t80) REVERT: A 1084 MET cc_start: 0.6244 (mmp) cc_final: 0.5996 (mmp) REVERT: A 1106 LYS cc_start: 0.6796 (ttmm) cc_final: 0.6328 (mttt) REVERT: A 1149 MET cc_start: 0.6995 (ttm) cc_final: 0.6655 (ttm) REVERT: A 1467 MET cc_start: 0.4756 (ptm) cc_final: 0.4401 (ptp) REVERT: B 232 LYS cc_start: 0.6401 (OUTLIER) cc_final: 0.6038 (mmtt) REVERT: B 279 GLU cc_start: 0.6275 (mt-10) cc_final: 0.5994 (mt-10) REVERT: B 413 ASN cc_start: 0.6741 (m-40) cc_final: 0.6541 (t0) REVERT: B 585 TYR cc_start: 0.6092 (m-80) cc_final: 0.5826 (m-80) REVERT: B 660 HIS cc_start: 0.6832 (t-90) cc_final: 0.6630 (t70) REVERT: B 745 PHE cc_start: 0.6846 (m-80) cc_final: 0.6531 (m-80) REVERT: B 932 MET cc_start: 0.6008 (mmt) cc_final: 0.5655 (mmp) REVERT: B 1051 LEU cc_start: 0.8250 (tp) cc_final: 0.7805 (mp) REVERT: B 1082 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6787 (tp) REVERT: B 1084 MET cc_start: 0.6213 (mmp) cc_final: 0.5931 (mmp) REVERT: B 1106 LYS cc_start: 0.6818 (ttmm) cc_final: 0.6339 (mttt) REVERT: B 1149 MET cc_start: 0.6927 (ttm) cc_final: 0.6613 (ttm) REVERT: B 1157 MET cc_start: 0.5933 (ttt) cc_final: 0.5637 (tmm) REVERT: B 1467 MET cc_start: 0.4765 (ptm) cc_final: 0.4393 (ptp) REVERT: C 232 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.6059 (mmtt) REVERT: C 279 GLU cc_start: 0.6283 (mt-10) cc_final: 0.6002 (mt-10) REVERT: C 585 TYR cc_start: 0.6078 (m-80) cc_final: 0.5814 (m-80) REVERT: C 660 HIS cc_start: 0.6894 (t-90) cc_final: 0.6600 (t-90) REVERT: C 745 PHE cc_start: 0.6845 (m-80) cc_final: 0.6533 (m-80) REVERT: C 1051 LEU cc_start: 0.8247 (tp) cc_final: 0.7806 (mp) REVERT: C 1082 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6785 (tp) REVERT: C 1084 MET cc_start: 0.6210 (mmp) cc_final: 0.5932 (mmp) REVERT: C 1106 LYS cc_start: 0.6793 (ttmm) cc_final: 0.6375 (mttt) REVERT: C 1141 ASP cc_start: 0.6694 (m-30) cc_final: 0.6264 (m-30) REVERT: C 1149 MET cc_start: 0.6966 (ttm) cc_final: 0.6725 (ttm) REVERT: C 1157 MET cc_start: 0.5909 (ttt) cc_final: 0.5620 (tmm) REVERT: C 1467 MET cc_start: 0.4761 (ptm) cc_final: 0.4394 (ptp) REVERT: D 232 LYS cc_start: 0.6423 (OUTLIER) cc_final: 0.6046 (mmtt) REVERT: D 279 GLU cc_start: 0.6281 (mt-10) cc_final: 0.6003 (mt-10) REVERT: D 585 TYR cc_start: 0.6097 (m-80) cc_final: 0.5822 (m-80) REVERT: D 660 HIS cc_start: 0.6898 (t-90) cc_final: 0.6602 (t-90) REVERT: D 745 PHE cc_start: 0.6843 (m-80) cc_final: 0.6375 (m-10) REVERT: D 1051 LEU cc_start: 0.8259 (tp) cc_final: 0.7812 (mp) REVERT: D 1082 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6791 (tp) REVERT: D 1084 MET cc_start: 0.6233 (mmp) cc_final: 0.5960 (mmp) REVERT: D 1106 LYS cc_start: 0.6788 (ttmm) cc_final: 0.6313 (mttt) REVERT: D 1141 ASP cc_start: 0.6771 (m-30) cc_final: 0.6359 (m-30) REVERT: D 1467 MET cc_start: 0.4771 (ptm) cc_final: 0.4407 (ptp) outliers start: 88 outliers final: 38 residues processed: 490 average time/residue: 0.2043 time to fit residues: 167.5662 Evaluate side-chains 443 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 397 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 552 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1156 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 306 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 509 optimal weight: 6.9990 chunk 513 optimal weight: 0.0370 chunk 104 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN A 660 HIS A1055 GLN B 280 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 ASN B1055 GLN C 280 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN C1055 GLN D 280 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 ASN D1055 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.172294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.140946 restraints weight = 57182.452| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.01 r_work: 0.3471 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39023 Z= 0.193 Angle : 0.577 7.868 53388 Z= 0.304 Chirality : 0.041 0.162 6324 Planarity : 0.005 0.048 6868 Dihedral : 5.727 74.917 6492 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.70 % Allowed : 11.48 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.11), residues: 5368 helix: 1.44 (0.09), residues: 2972 sheet: -1.47 (0.23), residues: 384 loop : -0.19 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 594 TYR 0.016 0.002 TYR B1057 PHE 0.024 0.002 PHE C 856 TRP 0.012 0.002 TRP A 620 HIS 0.021 0.002 HIS D1156 Details of bonding type rmsd covalent geometry : bond 0.00449 (39020) covalent geometry : angle 0.57704 (53372) SS BOND : bond 0.00133 ( 3) SS BOND : angle 0.19577 ( 16) hydrogen bonds : bond 0.04742 ( 2332) hydrogen bonds : angle 4.30721 ( 6864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 439 time to evaluate : 1.389 Fit side-chains REVERT: A 232 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6106 (mmtt) REVERT: A 279 GLU cc_start: 0.6261 (mt-10) cc_final: 0.6019 (mt-10) REVERT: A 413 ASN cc_start: 0.6761 (m-40) cc_final: 0.6536 (t0) REVERT: A 745 PHE cc_start: 0.6827 (m-80) cc_final: 0.6586 (m-80) REVERT: A 1083 PHE cc_start: 0.6153 (t80) cc_final: 0.5876 (t80) REVERT: A 1106 LYS cc_start: 0.6812 (ttmm) cc_final: 0.6269 (mttt) REVERT: A 1467 MET cc_start: 0.4889 (ptm) cc_final: 0.4361 (ptp) REVERT: B 129 MET cc_start: 0.5534 (tpt) cc_final: 0.4903 (tpp) REVERT: B 232 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6091 (mmtt) REVERT: B 413 ASN cc_start: 0.6814 (m-40) cc_final: 0.6557 (t0) REVERT: B 745 PHE cc_start: 0.6809 (m-80) cc_final: 0.6550 (m-80) REVERT: B 1083 PHE cc_start: 0.6260 (t80) cc_final: 0.5935 (t80) REVERT: B 1084 MET cc_start: 0.6189 (mmp) cc_final: 0.5735 (mmp) REVERT: B 1106 LYS cc_start: 0.6787 (ttmm) cc_final: 0.6293 (mttt) REVERT: B 1467 MET cc_start: 0.4894 (ptm) cc_final: 0.4350 (ptp) REVERT: C 129 MET cc_start: 0.5544 (tpt) cc_final: 0.4921 (tpp) REVERT: C 232 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6116 (mmtt) REVERT: C 660 HIS cc_start: 0.6913 (t-90) cc_final: 0.6620 (t-90) REVERT: C 745 PHE cc_start: 0.6813 (m-80) cc_final: 0.6553 (m-80) REVERT: C 1083 PHE cc_start: 0.6265 (t80) cc_final: 0.5940 (t80) REVERT: C 1084 MET cc_start: 0.6182 (mmp) cc_final: 0.5727 (mmp) REVERT: C 1106 LYS cc_start: 0.6815 (ttmm) cc_final: 0.6270 (mttt) REVERT: C 1467 MET cc_start: 0.4869 (ptm) cc_final: 0.4336 (ptp) REVERT: D 232 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6109 (mmtt) REVERT: D 660 HIS cc_start: 0.6920 (t-90) cc_final: 0.6627 (t-90) REVERT: D 745 PHE cc_start: 0.6810 (m-80) cc_final: 0.6557 (m-80) REVERT: D 1083 PHE cc_start: 0.6356 (t80) cc_final: 0.5717 (t80) REVERT: D 1084 MET cc_start: 0.6205 (mmp) cc_final: 0.5760 (mmp) REVERT: D 1106 LYS cc_start: 0.6772 (ttmm) cc_final: 0.6266 (mttt) REVERT: D 1467 MET cc_start: 0.4868 (ptm) cc_final: 0.4342 (ptp) outliers start: 85 outliers final: 68 residues processed: 501 average time/residue: 0.2142 time to fit residues: 178.6571 Evaluate side-chains 488 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 416 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1354 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1354 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1156 HIS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1354 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 425 optimal weight: 0.8980 chunk 431 optimal weight: 2.9990 chunk 414 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 505 optimal weight: 0.0010 chunk 158 optimal weight: 5.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.173485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.142457 restraints weight = 56953.285| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.04 r_work: 0.3477 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39023 Z= 0.137 Angle : 0.502 6.503 53388 Z= 0.264 Chirality : 0.039 0.143 6324 Planarity : 0.004 0.044 6868 Dihedral : 5.247 64.605 6492 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.02 % Allowed : 11.67 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.12 (0.11), residues: 5368 helix: 1.76 (0.09), residues: 2968 sheet: -1.75 (0.23), residues: 392 loop : -0.18 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 594 TYR 0.017 0.002 TYR C 330 PHE 0.015 0.002 PHE D1442 TRP 0.012 0.002 TRP A1052 HIS 0.005 0.001 HIS D1156 Details of bonding type rmsd covalent geometry : bond 0.00314 (39020) covalent geometry : angle 0.50180 (53372) SS BOND : bond 0.00085 ( 3) SS BOND : angle 0.16424 ( 16) hydrogen bonds : bond 0.04135 ( 2332) hydrogen bonds : angle 4.09331 ( 6864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 433 time to evaluate : 1.422 Fit side-chains REVERT: A 232 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6141 (mmtt) REVERT: A 279 GLU cc_start: 0.6232 (mt-10) cc_final: 0.6017 (mt-10) REVERT: A 413 ASN cc_start: 0.6707 (m-40) cc_final: 0.6471 (t0) REVERT: A 745 PHE cc_start: 0.6765 (m-80) cc_final: 0.6509 (m-80) REVERT: A 849 GLU cc_start: 0.6618 (tp30) cc_final: 0.6286 (tp30) REVERT: A 1083 PHE cc_start: 0.6161 (t80) cc_final: 0.5543 (t80) REVERT: A 1084 MET cc_start: 0.6147 (mmp) cc_final: 0.5828 (mmp) REVERT: A 1106 LYS cc_start: 0.6813 (ttmm) cc_final: 0.6299 (mttt) REVERT: A 1149 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5909 (ttm) REVERT: A 1467 MET cc_start: 0.4990 (ptm) cc_final: 0.4701 (ptp) REVERT: B 232 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6044 (mmtt) REVERT: B 413 ASN cc_start: 0.6783 (m-40) cc_final: 0.6523 (t0) REVERT: B 477 LYS cc_start: 0.7437 (mmmm) cc_final: 0.7026 (mtpp) REVERT: B 745 PHE cc_start: 0.6761 (m-80) cc_final: 0.6507 (m-80) REVERT: B 849 GLU cc_start: 0.6631 (tp30) cc_final: 0.6293 (tp30) REVERT: B 1051 LEU cc_start: 0.8236 (tp) cc_final: 0.7773 (mp) REVERT: B 1083 PHE cc_start: 0.6452 (t80) cc_final: 0.5947 (t80) REVERT: B 1084 MET cc_start: 0.6272 (mmp) cc_final: 0.5906 (mmp) REVERT: B 1106 LYS cc_start: 0.6808 (ttmm) cc_final: 0.6278 (mttt) REVERT: B 1467 MET cc_start: 0.4998 (ptm) cc_final: 0.4686 (ptp) REVERT: C 232 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6109 (mmtt) REVERT: C 477 LYS cc_start: 0.7417 (mmmm) cc_final: 0.7020 (mtpp) REVERT: C 745 PHE cc_start: 0.6768 (m-80) cc_final: 0.6524 (m-80) REVERT: C 849 GLU cc_start: 0.6650 (tp30) cc_final: 0.6314 (tp30) REVERT: C 1051 LEU cc_start: 0.8236 (tp) cc_final: 0.7772 (mp) REVERT: C 1083 PHE cc_start: 0.6468 (t80) cc_final: 0.5967 (t80) REVERT: C 1084 MET cc_start: 0.6248 (mmp) cc_final: 0.5883 (mmp) REVERT: C 1106 LYS cc_start: 0.6804 (ttmm) cc_final: 0.6294 (mttt) REVERT: C 1149 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.6064 (ttp) REVERT: C 1467 MET cc_start: 0.4988 (ptm) cc_final: 0.4692 (ptp) REVERT: D 232 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6068 (mmtt) REVERT: D 745 PHE cc_start: 0.6761 (m-80) cc_final: 0.6515 (m-80) REVERT: D 849 GLU cc_start: 0.6636 (tp30) cc_final: 0.6303 (tp30) REVERT: D 1051 LEU cc_start: 0.8239 (tp) cc_final: 0.7772 (mp) REVERT: D 1083 PHE cc_start: 0.6475 (t80) cc_final: 0.5969 (t80) REVERT: D 1084 MET cc_start: 0.6264 (mmp) cc_final: 0.5905 (mmp) REVERT: D 1106 LYS cc_start: 0.6821 (ttmm) cc_final: 0.6276 (mttt) REVERT: D 1467 MET cc_start: 0.4979 (ptm) cc_final: 0.4688 (ptp) outliers start: 95 outliers final: 62 residues processed: 500 average time/residue: 0.2258 time to fit residues: 188.4280 Evaluate side-chains 472 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 404 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 MET Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1354 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1149 MET Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1354 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1354 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 413 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 440 optimal weight: 4.9990 chunk 377 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 442 optimal weight: 0.9990 chunk 538 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 420 optimal weight: 0.9980 chunk 289 optimal weight: 6.9990 chunk 460 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 ASN A 702 ASN A1479 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN B1479 HIS C 440 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN ** C 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 ASN D 702 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.172223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.141559 restraints weight = 56863.728| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.14 r_work: 0.3466 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 39023 Z= 0.202 Angle : 0.592 6.712 53388 Z= 0.310 Chirality : 0.041 0.167 6324 Planarity : 0.005 0.053 6868 Dihedral : 5.625 58.137 6492 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.31 % Allowed : 11.93 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.66 (0.11), residues: 5368 helix: 1.43 (0.09), residues: 2972 sheet: -2.08 (0.23), residues: 388 loop : -0.45 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 805 TYR 0.016 0.002 TYR C1057 PHE 0.020 0.002 PHE D 278 TRP 0.013 0.002 TRP C 96 HIS 0.006 0.001 HIS A1470 Details of bonding type rmsd covalent geometry : bond 0.00474 (39020) covalent geometry : angle 0.59201 (53372) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.26403 ( 16) hydrogen bonds : bond 0.04868 ( 2332) hydrogen bonds : angle 4.38026 ( 6864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 428 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 ASP cc_start: 0.7009 (m-30) cc_final: 0.6757 (m-30) REVERT: A 849 GLU cc_start: 0.6621 (tp30) cc_final: 0.6291 (tp30) REVERT: A 1082 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6241 (tp) REVERT: A 1083 PHE cc_start: 0.6261 (t80) cc_final: 0.5661 (t80) REVERT: A 1084 MET cc_start: 0.6063 (mmp) cc_final: 0.5824 (mmp) REVERT: A 1106 LYS cc_start: 0.6786 (ttmm) cc_final: 0.6339 (mttt) REVERT: A 1467 MET cc_start: 0.4969 (ptm) cc_final: 0.4630 (ptp) REVERT: B 849 GLU cc_start: 0.6613 (tp30) cc_final: 0.6271 (tp30) REVERT: B 916 ARG cc_start: 0.7724 (ttt90) cc_final: 0.7510 (ttt90) REVERT: B 1083 PHE cc_start: 0.6331 (t80) cc_final: 0.5994 (t80) REVERT: B 1084 MET cc_start: 0.6289 (mmp) cc_final: 0.6000 (mmp) REVERT: B 1106 LYS cc_start: 0.6795 (ttmm) cc_final: 0.6269 (mttt) REVERT: B 1157 MET cc_start: 0.6239 (tmm) cc_final: 0.5672 (tmm) REVERT: B 1438 THR cc_start: 0.3294 (m) cc_final: 0.3091 (t) REVERT: B 1467 MET cc_start: 0.4902 (ptm) cc_final: 0.4507 (ptp) REVERT: C 663 LYS cc_start: 0.7591 (tmmt) cc_final: 0.7310 (pttp) REVERT: C 741 PHE cc_start: 0.6622 (t80) cc_final: 0.6308 (t80) REVERT: C 849 GLU cc_start: 0.6631 (tp30) cc_final: 0.6289 (tp30) REVERT: C 916 ARG cc_start: 0.7722 (ttt90) cc_final: 0.7509 (ttt90) REVERT: C 1083 PHE cc_start: 0.6338 (t80) cc_final: 0.6000 (t80) REVERT: C 1084 MET cc_start: 0.6273 (mmp) cc_final: 0.5986 (mmp) REVERT: C 1106 LYS cc_start: 0.6790 (ttmm) cc_final: 0.6343 (mttt) REVERT: C 1149 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.5940 (ttm) REVERT: C 1157 MET cc_start: 0.6120 (tmm) cc_final: 0.5517 (tmm) REVERT: C 1438 THR cc_start: 0.3300 (m) cc_final: 0.3094 (t) REVERT: C 1467 MET cc_start: 0.4963 (ptm) cc_final: 0.4570 (ptp) REVERT: D 663 LYS cc_start: 0.7581 (tmmt) cc_final: 0.7299 (pttp) REVERT: D 849 GLU cc_start: 0.6614 (tp30) cc_final: 0.6266 (tp30) REVERT: D 916 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7518 (ttt90) REVERT: D 1083 PHE cc_start: 0.6364 (t80) cc_final: 0.6024 (t80) REVERT: D 1084 MET cc_start: 0.6273 (mmp) cc_final: 0.5991 (mmp) REVERT: D 1106 LYS cc_start: 0.6786 (ttmm) cc_final: 0.6300 (mtpt) REVERT: D 1467 MET cc_start: 0.4963 (ptm) cc_final: 0.4572 (ptp) outliers start: 104 outliers final: 80 residues processed: 507 average time/residue: 0.2208 time to fit residues: 186.8754 Evaluate side-chains 483 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 401 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1155 GLU Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1354 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 MET Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1354 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 897 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1087 LEU Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1354 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 220 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 454 optimal weight: 0.7980 chunk 447 optimal weight: 2.9990 chunk 359 optimal weight: 0.5980 chunk 327 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 229 optimal weight: 0.5980 chunk 439 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN C 448 ASN C1479 HIS D 448 ASN D1479 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.174463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143154 restraints weight = 56854.153| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.80 r_work: 0.3508 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39023 Z= 0.102 Angle : 0.454 7.286 53388 Z= 0.240 Chirality : 0.037 0.133 6324 Planarity : 0.003 0.039 6868 Dihedral : 4.799 55.140 6492 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.91 % Allowed : 13.77 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.26 (0.12), residues: 5368 helix: 2.01 (0.09), residues: 2976 sheet: -2.12 (0.24), residues: 388 loop : -0.28 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 566 TYR 0.011 0.001 TYR C1057 PHE 0.015 0.001 PHE B1068 TRP 0.015 0.002 TRP C1052 HIS 0.004 0.001 HIS B1470 Details of bonding type rmsd covalent geometry : bond 0.00222 (39020) covalent geometry : angle 0.45437 (53372) SS BOND : bond 0.00046 ( 3) SS BOND : angle 0.14788 ( 16) hydrogen bonds : bond 0.03640 ( 2332) hydrogen bonds : angle 3.92108 ( 6864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 399 time to evaluate : 1.369 Fit side-chains REVERT: A 232 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.5954 (mttm) REVERT: A 849 GLU cc_start: 0.6546 (tp30) cc_final: 0.6338 (tp30) REVERT: A 1051 LEU cc_start: 0.8235 (tp) cc_final: 0.7744 (mp) REVERT: A 1083 PHE cc_start: 0.6307 (t80) cc_final: 0.5727 (t80) REVERT: A 1084 MET cc_start: 0.6066 (mmp) cc_final: 0.5845 (mmp) REVERT: A 1106 LYS cc_start: 0.6756 (ttmm) cc_final: 0.6284 (mttt) REVERT: A 1467 MET cc_start: 0.5134 (ptm) cc_final: 0.4714 (ptp) REVERT: B 232 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5938 (mttm) REVERT: B 849 GLU cc_start: 0.6542 (tp30) cc_final: 0.6224 (tp30) REVERT: B 932 MET cc_start: 0.5961 (mmt) cc_final: 0.5572 (mmp) REVERT: B 1051 LEU cc_start: 0.8232 (tp) cc_final: 0.7743 (mp) REVERT: B 1083 PHE cc_start: 0.6290 (t80) cc_final: 0.5952 (t80) REVERT: B 1084 MET cc_start: 0.6220 (mmp) cc_final: 0.5969 (mmp) REVERT: B 1106 LYS cc_start: 0.6770 (ttmm) cc_final: 0.6274 (mtpt) REVERT: B 1130 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5654 (mp0) REVERT: B 1157 MET cc_start: 0.6268 (tmm) cc_final: 0.5244 (tmm) REVERT: B 1467 MET cc_start: 0.4990 (ptm) cc_final: 0.4752 (ptp) REVERT: C 232 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.5944 (mttm) REVERT: C 849 GLU cc_start: 0.6549 (tp30) cc_final: 0.6228 (tp30) REVERT: C 1051 LEU cc_start: 0.8222 (tp) cc_final: 0.7739 (mp) REVERT: C 1084 MET cc_start: 0.6221 (mmp) cc_final: 0.5978 (mmp) REVERT: C 1106 LYS cc_start: 0.6764 (ttmm) cc_final: 0.6290 (mttt) REVERT: C 1157 MET cc_start: 0.6225 (tmm) cc_final: 0.5672 (tmm) REVERT: C 1467 MET cc_start: 0.5055 (ptm) cc_final: 0.4849 (ptp) REVERT: D 232 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.5919 (mttm) REVERT: D 849 GLU cc_start: 0.6543 (tp30) cc_final: 0.6221 (tp30) REVERT: D 1051 LEU cc_start: 0.8236 (tp) cc_final: 0.7747 (mp) REVERT: D 1084 MET cc_start: 0.6201 (mmp) cc_final: 0.5951 (mmp) REVERT: D 1106 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6292 (mtpt) REVERT: D 1467 MET cc_start: 0.5022 (ptm) cc_final: 0.4820 (ptp) outliers start: 60 outliers final: 45 residues processed: 445 average time/residue: 0.2033 time to fit residues: 152.1723 Evaluate side-chains 443 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 393 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1354 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1354 GLU Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 897 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1438 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 420 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 490 optimal weight: 2.9990 chunk 374 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 489 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 504 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.172504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.140607 restraints weight = 56635.013| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.80 r_work: 0.3476 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39023 Z= 0.187 Angle : 0.557 7.361 53388 Z= 0.291 Chirality : 0.041 0.228 6324 Planarity : 0.004 0.048 6868 Dihedral : 5.337 56.675 6492 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.32 % Allowed : 14.15 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.94 (0.12), residues: 5368 helix: 1.70 (0.09), residues: 2972 sheet: -2.23 (0.25), residues: 368 loop : -0.37 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D1161 TYR 0.019 0.002 TYR C 345 PHE 0.017 0.002 PHE A 880 TRP 0.012 0.002 TRP C 96 HIS 0.009 0.001 HIS B1470 Details of bonding type rmsd covalent geometry : bond 0.00436 (39020) covalent geometry : angle 0.55703 (53372) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.27249 ( 16) hydrogen bonds : bond 0.04549 ( 2332) hydrogen bonds : angle 4.23209 ( 6864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 407 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 849 GLU cc_start: 0.6615 (tp30) cc_final: 0.6289 (tp30) REVERT: A 1082 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6249 (tp) REVERT: A 1083 PHE cc_start: 0.6358 (t80) cc_final: 0.5759 (t80) REVERT: A 1084 MET cc_start: 0.6071 (mmp) cc_final: 0.5857 (mmp) REVERT: A 1106 LYS cc_start: 0.6797 (ttmm) cc_final: 0.6335 (mtpt) REVERT: A 1125 GLU cc_start: 0.6080 (mm-30) cc_final: 0.5717 (pt0) REVERT: A 1467 MET cc_start: 0.4979 (ptm) cc_final: 0.4775 (ptp) REVERT: B 849 GLU cc_start: 0.6584 (tp30) cc_final: 0.6253 (tp30) REVERT: B 1082 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6742 (tp) REVERT: B 1084 MET cc_start: 0.6235 (mmp) cc_final: 0.5972 (mmp) REVERT: B 1106 LYS cc_start: 0.6737 (ttmm) cc_final: 0.6291 (mtpt) REVERT: B 1157 MET cc_start: 0.6279 (tmm) cc_final: 0.5215 (tmm) REVERT: B 1467 MET cc_start: 0.4831 (ptm) cc_final: 0.4594 (ptp) REVERT: C 849 GLU cc_start: 0.6589 (tp30) cc_final: 0.6257 (tp30) REVERT: C 1082 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6741 (tp) REVERT: C 1084 MET cc_start: 0.6232 (mmp) cc_final: 0.5972 (mmp) REVERT: C 1106 LYS cc_start: 0.6820 (ttmm) cc_final: 0.6356 (mtpt) REVERT: C 1157 MET cc_start: 0.6238 (tmm) cc_final: 0.5664 (tmm) REVERT: C 1467 MET cc_start: 0.4885 (ptm) cc_final: 0.4655 (ptp) REVERT: D 849 GLU cc_start: 0.6601 (tp30) cc_final: 0.6268 (tp30) REVERT: D 1082 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6728 (tp) REVERT: D 1084 MET cc_start: 0.6205 (mmp) cc_final: 0.5951 (mmp) REVERT: D 1106 LYS cc_start: 0.6766 (ttmm) cc_final: 0.6310 (mtpt) REVERT: D 1467 MET cc_start: 0.4872 (ptm) cc_final: 0.4638 (ptp) outliers start: 73 outliers final: 64 residues processed: 463 average time/residue: 0.2140 time to fit residues: 166.6588 Evaluate side-chains 463 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 395 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1354 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 MET Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1354 GLU Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 897 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1438 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 206 optimal weight: 2.9990 chunk 477 optimal weight: 1.9990 chunk 100 optimal weight: 0.0060 chunk 250 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 393 optimal weight: 20.0000 chunk 327 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 427 optimal weight: 0.0970 chunk 416 optimal weight: 7.9990 chunk 43 optimal weight: 0.0170 overall best weight: 1.0236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 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 = 0.4308 r_free = 0.4308 target = 0.173823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.142136 restraints weight = 56919.480| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.90 r_work: 0.3490 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39023 Z= 0.117 Angle : 0.476 7.670 53388 Z= 0.250 Chirality : 0.038 0.165 6324 Planarity : 0.004 0.045 6868 Dihedral : 4.845 55.070 6492 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.54 % Allowed : 14.34 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.20 (0.12), residues: 5368 helix: 1.97 (0.09), residues: 2976 sheet: -2.39 (0.26), residues: 360 loop : -0.30 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 805 TYR 0.015 0.001 TYR C 345 PHE 0.012 0.001 PHE A 880 TRP 0.013 0.002 TRP C1052 HIS 0.008 0.001 HIS B1470 Details of bonding type rmsd covalent geometry : bond 0.00266 (39020) covalent geometry : angle 0.47642 (53372) SS BOND : bond 0.00041 ( 3) SS BOND : angle 0.18060 ( 16) hydrogen bonds : bond 0.03816 ( 2332) hydrogen bonds : angle 3.97065 ( 6864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 408 time to evaluate : 1.330 Fit side-chains REVERT: A 849 GLU cc_start: 0.6614 (tp30) cc_final: 0.6312 (tp30) REVERT: A 1051 LEU cc_start: 0.8240 (tp) cc_final: 0.7745 (mp) REVERT: A 1082 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6264 (tp) REVERT: A 1083 PHE cc_start: 0.6418 (t80) cc_final: 0.5866 (t80) REVERT: A 1106 LYS cc_start: 0.6809 (ttmm) cc_final: 0.6345 (mtpt) REVERT: A 1125 GLU cc_start: 0.6048 (mm-30) cc_final: 0.5663 (pt0) REVERT: A 1130 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5660 (mp0) REVERT: A 1467 MET cc_start: 0.5016 (ptm) cc_final: 0.4809 (ptp) REVERT: B 232 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6035 (mttm) REVERT: B 849 GLU cc_start: 0.6604 (tp30) cc_final: 0.6289 (tp30) REVERT: B 1051 LEU cc_start: 0.8235 (tp) cc_final: 0.7745 (mp) REVERT: B 1084 MET cc_start: 0.6222 (mmp) cc_final: 0.5994 (mmp) REVERT: B 1106 LYS cc_start: 0.6700 (ttmm) cc_final: 0.6257 (mtpt) REVERT: B 1130 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5666 (mp0) REVERT: B 1147 MET cc_start: 0.7247 (mtp) cc_final: 0.6865 (ttm) REVERT: B 1149 MET cc_start: 0.6161 (ttt) cc_final: 0.5749 (ttp) REVERT: B 1157 MET cc_start: 0.6226 (tmm) cc_final: 0.5213 (tmm) REVERT: B 1467 MET cc_start: 0.4919 (ptm) cc_final: 0.4662 (ptp) REVERT: C 232 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6051 (mttm) REVERT: C 849 GLU cc_start: 0.6612 (tp30) cc_final: 0.6297 (tp30) REVERT: C 1051 LEU cc_start: 0.8233 (tp) cc_final: 0.7746 (mp) REVERT: C 1084 MET cc_start: 0.6197 (mmp) cc_final: 0.5963 (mmp) REVERT: C 1106 LYS cc_start: 0.6756 (ttmm) cc_final: 0.6308 (mtpt) REVERT: C 1130 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5782 (mp0) REVERT: C 1157 MET cc_start: 0.6224 (tmm) cc_final: 0.5657 (tmm) REVERT: C 1467 MET cc_start: 0.4932 (ptm) cc_final: 0.4652 (ptp) REVERT: D 232 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6247 (mttm) REVERT: D 849 GLU cc_start: 0.6586 (tp30) cc_final: 0.6266 (tp30) REVERT: D 1051 LEU cc_start: 0.8240 (tp) cc_final: 0.7749 (mp) REVERT: D 1084 MET cc_start: 0.6163 (mmp) cc_final: 0.5929 (mmp) REVERT: D 1106 LYS cc_start: 0.6771 (ttmm) cc_final: 0.6311 (mtpt) REVERT: D 1130 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5760 (mp0) REVERT: D 1467 MET cc_start: 0.4909 (ptm) cc_final: 0.4633 (ptp) outliers start: 80 outliers final: 63 residues processed: 472 average time/residue: 0.2221 time to fit residues: 176.0631 Evaluate side-chains 472 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 401 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1440 VAL Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1354 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 GLU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1354 GLU Chi-restraints excluded: chain C residue 1440 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 897 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1130 GLU Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1438 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 383 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 501 optimal weight: 0.9980 chunk 277 optimal weight: 9.9990 chunk 530 optimal weight: 20.0000 chunk 222 optimal weight: 3.9990 chunk 395 optimal weight: 20.0000 chunk 534 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 315 optimal weight: 0.6980 chunk 483 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.173205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.141206 restraints weight = 56465.504| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.96 r_work: 0.3490 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39023 Z= 0.139 Angle : 0.508 8.274 53388 Z= 0.266 Chirality : 0.039 0.201 6324 Planarity : 0.004 0.049 6868 Dihedral : 5.016 55.144 6492 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.45 % Allowed : 14.22 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.14 (0.12), residues: 5368 helix: 1.92 (0.09), residues: 2980 sheet: -2.45 (0.25), residues: 360 loop : -0.32 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 805 TYR 0.018 0.002 TYR D 345 PHE 0.014 0.001 PHE C 880 TRP 0.010 0.002 TRP D 96 HIS 0.009 0.001 HIS D1470 Details of bonding type rmsd covalent geometry : bond 0.00320 (39020) covalent geometry : angle 0.50817 (53372) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.19104 ( 16) hydrogen bonds : bond 0.04106 ( 2332) hydrogen bonds : angle 4.06077 ( 6864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 412 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: A 849 GLU cc_start: 0.6615 (tp30) cc_final: 0.6295 (tp30) REVERT: A 1082 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6277 (tp) REVERT: A 1083 PHE cc_start: 0.6599 (t80) cc_final: 0.6114 (t80) REVERT: A 1106 LYS cc_start: 0.6702 (ttmm) cc_final: 0.6338 (mtpt) REVERT: A 1125 GLU cc_start: 0.5988 (mm-30) cc_final: 0.5668 (pt0) REVERT: A 1467 MET cc_start: 0.4954 (ptm) cc_final: 0.4719 (ptp) REVERT: B 232 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6126 (mttm) REVERT: B 849 GLU cc_start: 0.6585 (tp30) cc_final: 0.6286 (tp30) REVERT: B 1084 MET cc_start: 0.6252 (mmp) cc_final: 0.6018 (mmp) REVERT: B 1106 LYS cc_start: 0.6754 (ttmm) cc_final: 0.6313 (mtpt) REVERT: B 1130 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5713 (mp0) REVERT: B 1149 MET cc_start: 0.6271 (ttt) cc_final: 0.6000 (ttm) REVERT: B 1467 MET cc_start: 0.4876 (ptm) cc_final: 0.4595 (ptp) REVERT: C 232 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6162 (mttm) REVERT: C 849 GLU cc_start: 0.6586 (tp30) cc_final: 0.6287 (tp30) REVERT: C 1084 MET cc_start: 0.6262 (mmp) cc_final: 0.6029 (mmp) REVERT: C 1106 LYS cc_start: 0.6727 (ttmm) cc_final: 0.6339 (mtpt) REVERT: C 1157 MET cc_start: 0.6149 (tmm) cc_final: 0.5583 (tmm) REVERT: C 1467 MET cc_start: 0.4922 (ptm) cc_final: 0.4622 (ptp) REVERT: D 232 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6331 (mttm) REVERT: D 849 GLU cc_start: 0.6576 (tp30) cc_final: 0.6266 (tp30) REVERT: D 1082 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6647 (tp) REVERT: D 1084 MET cc_start: 0.6237 (mmp) cc_final: 0.5997 (mmp) REVERT: D 1106 LYS cc_start: 0.6768 (ttmm) cc_final: 0.6314 (mtpt) REVERT: D 1467 MET cc_start: 0.4902 (ptm) cc_final: 0.4605 (ptp) outliers start: 77 outliers final: 67 residues processed: 473 average time/residue: 0.2328 time to fit residues: 185.4218 Evaluate side-chains 480 residues out of total 4624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 407 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1440 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 874 ILE Chi-restraints excluded: chain B residue 897 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1130 GLU Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1354 GLU Chi-restraints excluded: chain B residue 1490 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 701 ILE Chi-restraints excluded: chain C residue 897 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 MET Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1354 GLU Chi-restraints excluded: chain C residue 1440 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 602 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 897 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1354 GLU Chi-restraints excluded: chain D residue 1438 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 405 optimal weight: 0.4980 chunk 173 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 270 optimal weight: 10.0000 chunk 494 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 263 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 356 optimal weight: 3.9990 chunk 539 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 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 = 0.4300 r_free = 0.4300 target = 0.173134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.141844 restraints weight = 56891.960| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.02 r_work: 0.3475 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39023 Z= 0.145 Angle : 0.515 8.251 53388 Z= 0.270 Chirality : 0.039 0.205 6324 Planarity : 0.004 0.049 6868 Dihedral : 5.051 54.982 6492 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.58 % Allowed : 14.28 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.08 (0.12), residues: 5368 helix: 1.87 (0.09), residues: 2980 sheet: -2.48 (0.25), residues: 360 loop : -0.37 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 805 TYR 0.018 0.002 TYR C 345 PHE 0.014 0.001 PHE A 880 TRP 0.013 0.002 TRP A 96 HIS 0.008 0.001 HIS B1470 Details of bonding type rmsd covalent geometry : bond 0.00336 (39020) covalent geometry : angle 0.51491 (53372) SS BOND : bond 0.00119 ( 3) SS BOND : angle 0.22343 ( 16) hydrogen bonds : bond 0.04146 ( 2332) hydrogen bonds : angle 4.09385 ( 6864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9893.66 seconds wall clock time: 169 minutes 46.34 seconds (10186.34 seconds total)