Starting phenix.real_space_refine on Mon Aug 10 01:44:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srg_40730/08_2026/8srg_40730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srg_40730/08_2026/8srg_40730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8srg_40730/08_2026/8srg_40730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srg_40730/08_2026/8srg_40730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8srg_40730/08_2026/8srg_40730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srg_40730/08_2026/8srg_40730.map" } resolution = 3.03 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= 0.204 sd= 1.234 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 16 5.21 5 S 208 5.16 5 C 25900 2.51 5 N 6960 2.21 5 O 6884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39976 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9869 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 295} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 987 Unresolved non-hydrogen angles: 1226 Unresolved non-hydrogen dihedrals: 793 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLU:plan': 42, 'ASP:plan': 56, 'GLN:plan1': 14, 'ARG:plan': 18, 'ASN:plan1': 18, 'HIS:plan': 7, 'TYR:plan': 4, 'TRP:plan': 1, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 644 Chain: "D" Number of atoms: 9869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9869 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 295} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 987 Unresolved non-hydrogen angles: 1226 Unresolved non-hydrogen dihedrals: 793 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLU:plan': 42, 'ASP:plan': 56, 'GLN:plan1': 14, 'ARG:plan': 18, 'ASN:plan1': 18, 'HIS:plan': 7, 'TYR:plan': 4, 'TRP:plan': 1, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 644 Chain: "A" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 125 Unusual residues: {' MG': 4, 'AMP%rna3p': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Chain: "D" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 125 Unusual residues: {' MG': 4, 'AMP%rna3p': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Restraints were copied for chains: B, C Time building chain proxies: 15.53, per 1000 atoms: 0.39 Number of scatterers: 39976 At special positions: 0 Unit cell: (159.418, 159.418, 186.676, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 208 16.00 P 8 15.00 Mg 16 11.99 O 6884 8.00 N 6960 7.00 C 25900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, 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 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 B1291 " - pdb=" SG CYS B1291 " distance=0.00 Simple disulfide: pdb=" SG CYS B1424 " - pdb=" SG CYS B1424 " 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: 3.26 Conformation dependent library (CDL) restraints added in 1.4 seconds 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10280 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 36 sheets defined 60.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.512A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.604A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.916A 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 removed outlier: 3.774A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.654A pdb=" N PHE A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.723A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.553A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.565A pdb=" N ILE A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.653A pdb=" N PHE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.823A 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: 3.518A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.555A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 3.560A pdb=" N ARG A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.557A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.956A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 585 " --> pdb=" O ASP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.593A pdb=" N ARG A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 599 " --> pdb=" O ARG A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.662A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.655A pdb=" N GLN A 647 " --> pdb=" O ARG A 644 " (cutoff:3.500A) 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: 3.656A pdb=" N PHE A 695 " --> pdb=" O ASN A 692 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.636A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 799 removed outlier: 3.530A pdb=" N ARG A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 removed outlier: 3.520A pdb=" N ARG A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 857 Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.911A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.505A 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: 4.034A 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: 3.866A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.667A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.408A 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: 5.819A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 4.143A 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 1168 Processing helix chain 'A' and resid 1202 through 1206 removed outlier: 3.538A pdb=" N ALA A1205 " --> pdb=" O SER A1202 " (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 1414 Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.756A pdb=" N ARG A1452 " --> pdb=" O ARG A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1490 Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.512A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.604A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.916A 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 removed outlier: 3.774A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.654A pdb=" N PHE B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.723A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.553A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 3.565A pdb=" N ILE B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 removed outlier: 3.653A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.823A 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: 3.518A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.555A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 3.560A pdb=" N ARG B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.557A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.956A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.593A pdb=" N ARG B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 599 " --> pdb=" O ARG B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 642 removed outlier: 3.662A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.655A pdb=" N GLN B 647 " --> pdb=" O ARG B 644 " (cutoff:3.500A) 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: 3.656A pdb=" N PHE B 695 " --> pdb=" O ASN B 692 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.636A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 799 removed outlier: 3.531A pdb=" N ARG B 792 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 removed outlier: 3.520A pdb=" N ARG B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 857 Processing helix chain 'B' and resid 859 through 866 removed outlier: 3.911A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.505A 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: 4.034A 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: 3.866A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.667A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.408A 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: 5.819A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 4.143A 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 1168 Processing helix chain 'B' and resid 1202 through 1206 removed outlier: 3.537A pdb=" N ALA B1205 " --> pdb=" O SER B1202 " (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 1414 Processing helix chain 'B' and resid 1447 through 1452 removed outlier: 3.756A pdb=" N ARG B1452 " --> pdb=" O ARG B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1478 through 1490 Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.512A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.604A pdb=" N LYS C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.916A 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 removed outlier: 3.774A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.654A pdb=" N PHE C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 358 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.724A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 407 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.554A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.565A pdb=" N ILE C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.654A pdb=" N PHE C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.823A 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: 3.517A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.556A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 removed outlier: 3.560A pdb=" N ARG C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.557A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.956A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 585 " --> pdb=" O ASP C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.593A pdb=" N ARG C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 599 " --> pdb=" O ARG C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 642 removed outlier: 3.662A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.655A pdb=" N GLN C 647 " --> pdb=" O ARG C 644 " (cutoff:3.500A) 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: 3.656A pdb=" N PHE C 695 " --> pdb=" O ASN C 692 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.636A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 799 removed outlier: 3.530A pdb=" N ARG C 792 " --> pdb=" O ALA C 788 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 removed outlier: 3.520A pdb=" N ARG C 805 " --> pdb=" O ALA C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 857 Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.911A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.505A 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: 4.034A 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: 3.866A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.667A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.408A 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: 5.819A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 4.143A 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 1168 Processing helix chain 'C' and resid 1202 through 1206 removed outlier: 3.538A pdb=" N ALA C1205 " --> pdb=" O SER C1202 " (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 1414 Processing helix chain 'C' and resid 1447 through 1452 removed outlier: 3.755A pdb=" N ARG C1452 " --> pdb=" O ARG C1448 " (cutoff:3.500A) Processing helix chain 'C' and resid 1478 through 1490 Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.512A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.604A pdb=" N LYS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 3.916A 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 removed outlier: 3.774A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.654A pdb=" N PHE D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 358 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.723A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.553A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 3.565A pdb=" N ILE D 443 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.654A pdb=" N PHE D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.823A 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: 3.518A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.555A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 removed outlier: 3.560A pdb=" N ARG D 553 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.557A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.956A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR D 585 " --> pdb=" O ASP D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.593A pdb=" N ARG D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D 599 " --> pdb=" O ARG D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 642 removed outlier: 3.662A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.655A pdb=" N GLN D 647 " --> pdb=" O ARG D 644 " (cutoff:3.500A) 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: 3.656A pdb=" N PHE D 695 " --> pdb=" O ASN D 692 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.636A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 799 removed outlier: 3.530A pdb=" N ARG D 792 " --> pdb=" O ALA D 788 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 removed outlier: 3.520A pdb=" N ARG D 805 " --> pdb=" O ALA D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 857 Processing helix chain 'D' and resid 859 through 866 removed outlier: 3.911A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.505A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 4.034A 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: 3.866A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.667A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.408A 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: 5.819A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 4.143A 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 1168 Processing helix chain 'D' and resid 1202 through 1206 removed outlier: 3.538A pdb=" N ALA D1205 " --> pdb=" O SER D1202 " (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 1414 Processing helix chain 'D' and resid 1447 through 1452 removed outlier: 3.756A pdb=" N ARG D1452 " --> pdb=" O ARG D1448 " (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: 6.378A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1200 removed outlier: 7.201A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY B1324 " --> pdb=" O TRP B1434 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU B1436 " --> pdb=" O GLY B1324 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN B1326 " --> pdb=" O GLU B1436 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR B1438 " --> pdb=" O ASN B1326 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA B1328 " --> pdb=" O THR B1438 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL B1440 " --> pdb=" O ALA B1328 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B1330 " --> pdb=" O VAL B1440 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE B1442 " --> pdb=" O ASP B1330 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B1332 " --> pdb=" O PHE B1442 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP B1444 " --> pdb=" O VAL B1332 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B1334 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 17.731A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.905A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.452A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.905A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.731A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1251 through 1252 removed outlier: 5.861A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1278 through 1281 Processing sheet with id=AA8, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 4.041A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.452A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.905A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.731A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.731A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.905A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1353 through 1360 current: chain 'A' and resid 1416 through 1423 Processing sheet with id=AB2, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB3, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AB4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB5, first strand: chain 'B' and resid 232 through 236 removed outlier: 6.378A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1199 through 1200 removed outlier: 7.201A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY C1324 " --> pdb=" O TRP C1434 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU C1436 " --> pdb=" O GLY C1324 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN C1326 " --> pdb=" O GLU C1436 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR C1438 " --> pdb=" O ASN C1326 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA C1328 " --> pdb=" O THR C1438 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL C1440 " --> pdb=" O ALA C1328 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP C1330 " --> pdb=" O VAL C1440 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE C1442 " --> pdb=" O ASP C1330 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL C1332 " --> pdb=" O PHE C1442 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASP C1444 " --> pdb=" O VAL C1332 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C1334 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 17.732A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.906A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.452A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.906A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.732A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1251 through 1252 removed outlier: 5.861A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1278 through 1281 Processing sheet with id=AC1, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 4.041A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AC3, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AC4, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AC5, first strand: chain 'C' and resid 232 through 236 removed outlier: 6.378A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1199 through 1200 removed outlier: 7.201A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY D1324 " --> pdb=" O TRP D1434 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU D1436 " --> pdb=" O GLY D1324 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN D1326 " --> pdb=" O GLU D1436 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR D1438 " --> pdb=" O ASN D1326 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA D1328 " --> pdb=" O THR D1438 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL D1440 " --> pdb=" O ALA D1328 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP D1330 " --> pdb=" O VAL D1440 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE D1442 " --> pdb=" O ASP D1330 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D1332 " --> pdb=" O PHE D1442 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP D1444 " --> pdb=" O VAL D1332 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR D1334 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 17.731A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.905A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.452A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.507A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.905A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.731A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 5.861A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1278 through 1281 Processing sheet with id=AD1, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 4.041A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD3, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AD4, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD5, first strand: chain 'D' and resid 232 through 236 removed outlier: 6.378A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1251 through 1252 removed outlier: 5.861A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 1278 through 1281 Processing sheet with id=AD8, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 4.041A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1346 through 1347 2339 hydrogen bonds defined for protein. 6837 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: 9.80 Time building geometry restraints manager: 4.28 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: 6301 1.32 - 1.44: 11135 1.44 - 1.57: 23096 1.57 - 1.70: 20 1.70 - 1.82: 372 Bond restraints: 40924 Sorted by residual: bond pdb=" C2 RP5 B1501 " pdb=" C3 RP5 B1501 " ideal model delta sigma weight residual 1.525 1.244 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C2 RP5 D6003 " pdb=" C3 RP5 D6003 " ideal model delta sigma weight residual 1.525 1.244 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C2 RP5 A1501 " pdb=" C3 RP5 A1501 " ideal model delta sigma weight residual 1.525 1.244 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C2 RP5 C1501 " pdb=" C3 RP5 C1501 " ideal model delta sigma weight residual 1.525 1.244 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C4 AMP C1502 " pdb=" C5 AMP C1502 " ideal model delta sigma weight residual 1.490 1.340 0.150 2.00e-02 2.50e+03 5.60e+01 ... (remaining 40919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 51609 2.90 - 5.81: 3759 5.81 - 8.71: 456 8.71 - 11.61: 92 11.61 - 14.52: 12 Bond angle restraints: 55928 Sorted by residual: angle pdb=" N ALA B 788 " pdb=" CA ALA B 788 " pdb=" C ALA B 788 " ideal model delta sigma weight residual 112.89 105.62 7.27 1.24e+00 6.50e-01 3.44e+01 angle pdb=" N ALA A 788 " pdb=" CA ALA A 788 " pdb=" C ALA A 788 " ideal model delta sigma weight residual 112.89 105.62 7.27 1.24e+00 6.50e-01 3.44e+01 angle pdb=" N ALA D 788 " pdb=" CA ALA D 788 " pdb=" C ALA D 788 " ideal model delta sigma weight residual 112.89 105.62 7.27 1.24e+00 6.50e-01 3.44e+01 angle pdb=" N ALA C 788 " pdb=" CA ALA C 788 " pdb=" C ALA C 788 " ideal model delta sigma weight residual 112.89 105.62 7.27 1.24e+00 6.50e-01 3.44e+01 angle pdb=" CA ILE C 864 " pdb=" CB ILE C 864 " pdb=" CG2 ILE C 864 " ideal model delta sigma weight residual 110.50 119.18 -8.68 1.70e+00 3.46e-01 2.61e+01 ... (remaining 55923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 23815 26.91 - 53.81: 712 53.81 - 80.72: 92 80.72 - 107.62: 12 107.62 - 134.53: 4 Dihedral angle restraints: 24635 sinusoidal: 8771 harmonic: 15864 Sorted by residual: dihedral pdb=" C2' AMP D6004 " pdb=" C1' AMP D6004 " pdb=" N9 AMP D6004 " pdb=" C4 AMP D6004 " ideal model delta sinusoidal sigma weight residual 91.55 -42.97 134.53 1 2.00e+01 2.50e-03 4.08e+01 dihedral pdb=" C2' AMP B1502 " pdb=" C1' AMP B1502 " pdb=" N9 AMP B1502 " pdb=" C4 AMP B1502 " ideal model delta sinusoidal sigma weight residual 91.55 -42.97 134.53 1 2.00e+01 2.50e-03 4.08e+01 dihedral pdb=" C2' AMP A1502 " pdb=" C1' AMP A1502 " pdb=" N9 AMP A1502 " pdb=" C4 AMP A1502 " ideal model delta sinusoidal sigma weight residual 91.55 -42.97 134.53 1 2.00e+01 2.50e-03 4.08e+01 ... (remaining 24632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 5968 0.136 - 0.272: 520 0.272 - 0.408: 52 0.408 - 0.544: 16 0.544 - 0.680: 4 Chirality restraints: 6560 Sorted by residual: chirality pdb=" CG LEU B 323 " pdb=" CB LEU B 323 " pdb=" CD1 LEU B 323 " pdb=" CD2 LEU B 323 " both_signs ideal model delta sigma weight residual False -2.59 -1.91 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CG LEU D 323 " pdb=" CB LEU D 323 " pdb=" CD1 LEU D 323 " pdb=" CD2 LEU D 323 " both_signs ideal model delta sigma weight residual False -2.59 -1.91 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CG LEU A 323 " pdb=" CB LEU A 323 " pdb=" CD1 LEU A 323 " pdb=" CD2 LEU A 323 " both_signs ideal model delta sigma weight residual False -2.59 -1.91 -0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 6557 not shown) Planarity restraints: 7080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D1071 " -0.023 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ALA D1071 " 0.076 2.00e-02 2.50e+03 pdb=" O ALA D1071 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO D1072 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B1071 " 0.023 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ALA B1071 " -0.076 2.00e-02 2.50e+03 pdb=" O ALA B1071 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO B1072 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1071 " -0.023 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ALA A1071 " 0.076 2.00e-02 2.50e+03 pdb=" O ALA A1071 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO A1072 " -0.026 2.00e-02 2.50e+03 ... (remaining 7077 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 229 2.61 - 3.18: 30505 3.18 - 3.75: 61937 3.75 - 4.33: 82381 4.33 - 4.90: 140379 Nonbonded interactions: 315431 Sorted by model distance: nonbonded pdb=" SG CYS D 997 " pdb=" SG CYS D1006 " model vdw 2.033 3.760 nonbonded pdb=" O GLY C1370 " pdb="MG MG C1505 " model vdw 2.134 2.170 nonbonded pdb=" O GLY A1370 " pdb="MG MG A1505 " model vdw 2.134 2.170 nonbonded pdb=" O GLY B1370 " pdb="MG MG B1505 " model vdw 2.134 2.170 nonbonded pdb=" O GLY D1370 " pdb="MG MG D6007 " model vdw 2.134 2.170 ... (remaining 315426 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: 0.14 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 52 through 1494 or resid 1505 through 1506 or resid 1509)) \ selection = (chain 'B' and (resid 52 through 1494 or resid 1505 through 1506 or resid 1509)) \ selection = (chain 'C' and (resid 52 through 1494 or resid 1505 through 1506 or resid 1509)) \ selection = (chain 'D' and (resid 52 through 1494 or resid 6005 through 6006 or resid 6009)) \ } 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: 7.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 42.600 Find NCS groups from input model: 1.120 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 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 : 0.012 0.281 40927 Z= 0.657 Angle : 1.611 14.518 55945 Z= 1.012 Chirality : 0.085 0.680 6560 Planarity : 0.011 0.068 7080 Dihedral : 13.347 134.529 14324 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.57 % Allowed : 0.69 % Favored : 98.74 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 3.64 % 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: 0.61 (0.11), residues: 5424 helix: 1.02 (0.09), residues: 3016 sheet: -0.83 (0.23), residues: 400 loop : -0.12 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 655 TYR 0.042 0.006 TYR D1057 PHE 0.055 0.006 PHE C 941 TRP 0.023 0.003 TRP D1434 HIS 0.036 0.003 HIS D1255 Details of bonding type rmsd/Z covalent geometry : bond 0.01215 / 0.66 (40924) covalent geometry : angle 1.61083 / 1.01 (55928) SS BOND : bond 0.00183 / 0.08 ( 3) SS BOND : angle 1.21819 / 0.74 ( 17) hydrogen bonds : bond 0.15650 / 10.57 ( 2327) hydrogen bonds : angle 6.87600 / 5.01 ( 6837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 432 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.5407 (mmm) cc_final: 0.5025 (mmm) REVERT: A 173 GLN cc_start: 0.5756 (mt0) cc_final: 0.5453 (tm-30) REVERT: A 215 THR cc_start: 0.6667 (t) cc_final: 0.6362 (m) REVERT: A 271 GLU cc_start: 0.5486 (pm20) cc_final: 0.5095 (pp20) REVERT: A 448 ASN cc_start: 0.5595 (m-40) cc_final: 0.5020 (t0) REVERT: A 477 LYS cc_start: 0.7506 (mttp) cc_final: 0.7076 (mmtt) REVERT: A 523 ASN cc_start: 0.6747 (t0) cc_final: 0.6300 (p0) REVERT: A 683 MET cc_start: 0.6031 (tpp) cc_final: 0.5744 (tpp) REVERT: A 747 PHE cc_start: 0.4800 (m-80) cc_final: 0.4584 (m-80) REVERT: A 932 MET cc_start: 0.6291 (mmt) cc_final: 0.5791 (mmp) REVERT: A 1042 MET cc_start: 0.6361 (mtp) cc_final: 0.6105 (mtm) REVERT: A 1131 MET cc_start: 0.5307 (tpt) cc_final: 0.5047 (tpt) REVERT: A 1138 MET cc_start: 0.6252 (ttp) cc_final: 0.5871 (ttm) REVERT: A 1323 TRP cc_start: 0.6095 (m100) cc_final: 0.5857 (m100) REVERT: A 1434 TRP cc_start: 0.6634 (p90) cc_final: 0.6212 (p90) REVERT: B 76 MET cc_start: 0.5400 (mmm) cc_final: 0.5014 (mmm) REVERT: B 173 GLN cc_start: 0.5727 (mt0) cc_final: 0.5423 (tm-30) REVERT: B 215 THR cc_start: 0.6559 (t) cc_final: 0.6246 (m) REVERT: B 271 GLU cc_start: 0.5500 (pm20) cc_final: 0.5105 (pp20) REVERT: B 448 ASN cc_start: 0.5636 (m-40) cc_final: 0.5066 (t0) REVERT: B 477 LYS cc_start: 0.7475 (mttp) cc_final: 0.7063 (mmtt) REVERT: B 523 ASN cc_start: 0.6746 (t0) cc_final: 0.6298 (p0) REVERT: B 683 MET cc_start: 0.5912 (tpp) cc_final: 0.5642 (tpp) REVERT: B 747 PHE cc_start: 0.4797 (m-80) cc_final: 0.4582 (m-80) REVERT: B 932 MET cc_start: 0.6290 (mmt) cc_final: 0.5789 (mmp) REVERT: B 1042 MET cc_start: 0.6365 (mtp) cc_final: 0.6105 (mtm) REVERT: B 1131 MET cc_start: 0.5338 (tpt) cc_final: 0.5072 (tpt) REVERT: B 1138 MET cc_start: 0.6253 (ttp) cc_final: 0.5872 (ttm) REVERT: B 1155 GLU cc_start: 0.6912 (tp30) cc_final: 0.6661 (tp30) REVERT: B 1323 TRP cc_start: 0.6113 (m100) cc_final: 0.5870 (m100) REVERT: B 1434 TRP cc_start: 0.6638 (p90) cc_final: 0.6215 (p90) REVERT: C 76 MET cc_start: 0.5401 (mmm) cc_final: 0.5016 (mmm) REVERT: C 173 GLN cc_start: 0.5728 (mt0) cc_final: 0.5424 (tm-30) REVERT: C 215 THR cc_start: 0.6560 (t) cc_final: 0.6248 (m) REVERT: C 271 GLU cc_start: 0.5505 (pm20) cc_final: 0.5109 (pp20) REVERT: C 448 ASN cc_start: 0.5636 (m-40) cc_final: 0.5068 (t0) REVERT: C 477 LYS cc_start: 0.7475 (mttp) cc_final: 0.7063 (mmtt) REVERT: C 523 ASN cc_start: 0.6746 (t0) cc_final: 0.6298 (p0) REVERT: C 683 MET cc_start: 0.5912 (tpp) cc_final: 0.5640 (tpp) REVERT: C 747 PHE cc_start: 0.4790 (m-80) cc_final: 0.4575 (m-80) REVERT: C 932 MET cc_start: 0.6291 (mmt) cc_final: 0.5791 (mmp) REVERT: C 1042 MET cc_start: 0.6365 (mtp) cc_final: 0.6106 (mtm) REVERT: C 1131 MET cc_start: 0.5338 (tpt) cc_final: 0.5073 (tpt) REVERT: C 1138 MET cc_start: 0.6250 (ttp) cc_final: 0.5870 (ttm) REVERT: C 1155 GLU cc_start: 0.6915 (tp30) cc_final: 0.6661 (tp30) REVERT: C 1323 TRP cc_start: 0.6112 (m100) cc_final: 0.5862 (m100) REVERT: C 1434 TRP cc_start: 0.6639 (p90) cc_final: 0.6216 (p90) REVERT: D 76 MET cc_start: 0.5406 (mmm) cc_final: 0.5025 (mmm) REVERT: D 173 GLN cc_start: 0.5751 (mt0) cc_final: 0.5447 (tm-30) REVERT: D 215 THR cc_start: 0.6667 (t) cc_final: 0.6360 (m) REVERT: D 271 GLU cc_start: 0.5497 (pm20) cc_final: 0.5105 (pp20) REVERT: D 448 ASN cc_start: 0.5594 (m-40) cc_final: 0.5019 (t0) REVERT: D 477 LYS cc_start: 0.7472 (mttp) cc_final: 0.7061 (mmtt) REVERT: D 523 ASN cc_start: 0.6747 (t0) cc_final: 0.6300 (p0) REVERT: D 683 MET cc_start: 0.5962 (tpp) cc_final: 0.5685 (tpp) REVERT: D 747 PHE cc_start: 0.4765 (m-80) cc_final: 0.4548 (m-80) REVERT: D 932 MET cc_start: 0.6289 (mmt) cc_final: 0.5790 (mmp) REVERT: D 1042 MET cc_start: 0.6341 (mtp) cc_final: 0.6090 (mtm) REVERT: D 1131 MET cc_start: 0.5306 (tpt) cc_final: 0.5046 (tpt) REVERT: D 1138 MET cc_start: 0.6251 (ttp) cc_final: 0.5870 (ttm) REVERT: D 1323 TRP cc_start: 0.6097 (m100) cc_final: 0.5858 (m100) REVERT: D 1434 TRP cc_start: 0.6636 (p90) cc_final: 0.6213 (p90) outliers start: 20 outliers final: 0 residues processed: 448 average time/residue: 0.2478 time to fit residues: 179.3334 Evaluate side-chains 289 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 0.7980 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 702 ASN A1255 HIS B1255 HIS C 598 GLN C1255 HIS D 598 GLN D 702 ASN D1255 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.087121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.071721 restraints weight = 130053.625| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.29 r_work: 0.3289 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40927 Z= 0.127 Angle : 0.514 6.587 55945 Z= 0.266 Chirality : 0.038 0.128 6560 Planarity : 0.004 0.053 7080 Dihedral : 7.292 132.775 6716 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.75 % Allowed : 4.31 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.56 (0.11), residues: 5424 helix: 2.02 (0.09), residues: 3028 sheet: -0.60 (0.22), residues: 436 loop : -0.06 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 617 TYR 0.009 0.001 TYR D 917 PHE 0.014 0.002 PHE B1160 TRP 0.014 0.001 TRP B1124 HIS 0.007 0.001 HIS C1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (40924) covalent geometry : angle 0.51405 / 0.27 (55928) SS BOND : bond 0.00082 / 0.04 ( 3) SS BOND : angle 0.09206 / 0.06 ( 17) hydrogen bonds : bond 0.04168 / 2.84 ( 2327) hydrogen bonds : angle 3.98955 / 2.93 ( 6837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 1.572 Fit side-chains REVERT: A 76 MET cc_start: 0.6918 (mmm) cc_final: 0.6320 (mmm) REVERT: A 189 MET cc_start: 0.7239 (mtm) cc_final: 0.7023 (mtm) REVERT: A 271 GLU cc_start: 0.6548 (pm20) cc_final: 0.6185 (pp20) REVERT: A 272 ILE cc_start: 0.6431 (mp) cc_final: 0.6221 (mt) REVERT: A 448 ASN cc_start: 0.6667 (m-40) cc_final: 0.6238 (t0) REVERT: A 523 ASN cc_start: 0.7286 (t0) cc_final: 0.6871 (p0) REVERT: A 747 PHE cc_start: 0.5123 (m-80) cc_final: 0.4866 (m-80) REVERT: A 932 MET cc_start: 0.7859 (mmt) cc_final: 0.7611 (mmp) REVERT: A 934 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.5782 (mmt) REVERT: A 935 MET cc_start: 0.8496 (mmm) cc_final: 0.8263 (mmm) REVERT: A 1042 MET cc_start: 0.8064 (mtp) cc_final: 0.7755 (mtm) REVERT: A 1083 PHE cc_start: 0.5960 (t80) cc_final: 0.5446 (t80) REVERT: A 1126 ARG cc_start: 0.7083 (ttp-110) cc_final: 0.6593 (ttp-110) REVERT: A 1138 MET cc_start: 0.8095 (ttp) cc_final: 0.7793 (ttm) REVERT: A 1388 MET cc_start: 0.8187 (mmt) cc_final: 0.7948 (mmt) REVERT: B 76 MET cc_start: 0.6908 (mmm) cc_final: 0.6310 (mmm) REVERT: B 271 GLU cc_start: 0.6547 (pm20) cc_final: 0.6174 (pp20) REVERT: B 272 ILE cc_start: 0.6435 (mp) cc_final: 0.6226 (mt) REVERT: B 448 ASN cc_start: 0.6629 (m-40) cc_final: 0.6235 (t0) REVERT: B 477 LYS cc_start: 0.8026 (mttp) cc_final: 0.7793 (mmmm) REVERT: B 523 ASN cc_start: 0.7274 (t0) cc_final: 0.6870 (p0) REVERT: B 747 PHE cc_start: 0.5123 (m-80) cc_final: 0.4861 (m-80) REVERT: B 932 MET cc_start: 0.7876 (mmt) cc_final: 0.7629 (mmp) REVERT: B 934 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.5781 (mmt) REVERT: B 935 MET cc_start: 0.8503 (mmm) cc_final: 0.8271 (mmm) REVERT: B 1042 MET cc_start: 0.8061 (mtp) cc_final: 0.7752 (mtm) REVERT: B 1083 PHE cc_start: 0.5994 (t80) cc_final: 0.5486 (t80) REVERT: B 1126 ARG cc_start: 0.7099 (ttp-110) cc_final: 0.6607 (ttp-110) REVERT: B 1138 MET cc_start: 0.8114 (ttp) cc_final: 0.7814 (ttm) REVERT: B 1153 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8219 (tt) REVERT: B 1388 MET cc_start: 0.8182 (mmt) cc_final: 0.7942 (mmt) REVERT: C 76 MET cc_start: 0.6895 (mmm) cc_final: 0.6300 (mmm) REVERT: C 271 GLU cc_start: 0.6550 (pm20) cc_final: 0.6175 (pp20) REVERT: C 272 ILE cc_start: 0.6432 (mp) cc_final: 0.6223 (mt) REVERT: C 448 ASN cc_start: 0.6632 (m-40) cc_final: 0.6239 (t0) REVERT: C 477 LYS cc_start: 0.8018 (mttp) cc_final: 0.7789 (mmmm) REVERT: C 523 ASN cc_start: 0.7272 (t0) cc_final: 0.6867 (p0) REVERT: C 747 PHE cc_start: 0.5124 (m-80) cc_final: 0.4861 (m-80) REVERT: C 932 MET cc_start: 0.7892 (mmt) cc_final: 0.7646 (mmp) REVERT: C 934 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.5793 (mmt) REVERT: C 935 MET cc_start: 0.8494 (mmm) cc_final: 0.8263 (mmm) REVERT: C 1042 MET cc_start: 0.8058 (mtp) cc_final: 0.7746 (mtm) REVERT: C 1083 PHE cc_start: 0.5995 (t80) cc_final: 0.5490 (t80) REVERT: C 1126 ARG cc_start: 0.7102 (ttp-110) cc_final: 0.6602 (ttp-110) REVERT: C 1138 MET cc_start: 0.8117 (ttp) cc_final: 0.7816 (ttm) REVERT: C 1153 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8203 (tt) REVERT: C 1388 MET cc_start: 0.8185 (mmt) cc_final: 0.7943 (mmt) REVERT: D 76 MET cc_start: 0.6913 (mmm) cc_final: 0.6323 (mmm) REVERT: D 271 GLU cc_start: 0.6560 (pm20) cc_final: 0.6192 (pp20) REVERT: D 272 ILE cc_start: 0.6448 (mp) cc_final: 0.6234 (mt) REVERT: D 448 ASN cc_start: 0.6674 (m-40) cc_final: 0.6244 (t0) REVERT: D 523 ASN cc_start: 0.7280 (t0) cc_final: 0.6866 (p0) REVERT: D 572 PHE cc_start: 0.6094 (t80) cc_final: 0.5699 (t80) REVERT: D 747 PHE cc_start: 0.5128 (m-80) cc_final: 0.4872 (m-80) REVERT: D 932 MET cc_start: 0.7864 (mmt) cc_final: 0.7618 (mmp) REVERT: D 934 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.5776 (mmt) REVERT: D 935 MET cc_start: 0.8494 (mmm) cc_final: 0.8259 (mmm) REVERT: D 1042 MET cc_start: 0.8064 (mtp) cc_final: 0.7755 (mtm) REVERT: D 1083 PHE cc_start: 0.5953 (t80) cc_final: 0.5442 (t80) REVERT: D 1126 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6589 (ttp-110) REVERT: D 1138 MET cc_start: 0.8094 (ttp) cc_final: 0.7792 (ttm) REVERT: D 1157 MET cc_start: 0.8160 (mmp) cc_final: 0.7927 (mmp) REVERT: D 1388 MET cc_start: 0.8184 (mmt) cc_final: 0.7943 (mmt) outliers start: 26 outliers final: 14 residues processed: 327 average time/residue: 0.2252 time to fit residues: 124.6748 Evaluate side-chains 282 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 934 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 1153 LEU Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 934 MET Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 934 MET Chi-restraints excluded: chain D residue 1153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 295 optimal weight: 2.9990 chunk 484 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 438 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 903 HIS A1326 ASN C 903 HIS D 592 GLN D 903 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.085919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.070466 restraints weight = 129316.018| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.25 r_work: 0.3233 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40927 Z= 0.148 Angle : 0.537 7.100 55945 Z= 0.274 Chirality : 0.039 0.142 6560 Planarity : 0.004 0.056 7080 Dihedral : 6.796 133.489 6716 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.98 % Allowed : 6.98 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.53 (0.11), residues: 5424 helix: 2.05 (0.09), residues: 3048 sheet: -0.86 (0.23), residues: 428 loop : -0.14 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 612 TYR 0.012 0.002 TYR B 917 PHE 0.018 0.002 PHE C 736 TRP 0.016 0.002 TRP B1216 HIS 0.005 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (40924) covalent geometry : angle 0.53726 / 0.27 (55928) SS BOND : bond 0.00110 / 0.05 ( 3) SS BOND : angle 0.12450 / 0.08 ( 17) hydrogen bonds : bond 0.04070 / 2.80 ( 2327) hydrogen bonds : angle 3.84924 / 2.82 ( 6837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.994 Fit side-chains REVERT: A 76 MET cc_start: 0.7058 (mmm) cc_final: 0.6322 (mmm) REVERT: A 271 GLU cc_start: 0.6660 (pm20) cc_final: 0.6300 (pp20) REVERT: A 272 ILE cc_start: 0.6390 (mp) cc_final: 0.6132 (mt) REVERT: A 592 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: A 747 PHE cc_start: 0.5039 (m-80) cc_final: 0.4774 (m-80) REVERT: A 755 PHE cc_start: 0.3649 (m-80) cc_final: 0.3138 (m-80) REVERT: A 932 MET cc_start: 0.8076 (mmt) cc_final: 0.7582 (mmp) REVERT: A 934 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.5676 (mmt) REVERT: A 1083 PHE cc_start: 0.6030 (t80) cc_final: 0.5484 (t80) REVERT: A 1084 MET cc_start: 0.4800 (mmt) cc_final: 0.4591 (mmt) REVERT: A 1126 ARG cc_start: 0.7085 (ttp-110) cc_final: 0.6553 (ttp-110) REVERT: B 76 MET cc_start: 0.7064 (mmm) cc_final: 0.6325 (mmm) REVERT: B 271 GLU cc_start: 0.6661 (pm20) cc_final: 0.6287 (pp20) REVERT: B 272 ILE cc_start: 0.6397 (mp) cc_final: 0.6132 (mt) REVERT: B 477 LYS cc_start: 0.8131 (mttp) cc_final: 0.7857 (mttp) REVERT: B 747 PHE cc_start: 0.5029 (m-80) cc_final: 0.4763 (m-80) REVERT: B 755 PHE cc_start: 0.3608 (m-80) cc_final: 0.3091 (m-80) REVERT: B 932 MET cc_start: 0.8057 (mmt) cc_final: 0.7559 (mmp) REVERT: B 934 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.5692 (mmt) REVERT: B 1083 PHE cc_start: 0.6035 (t80) cc_final: 0.5487 (t80) REVERT: B 1084 MET cc_start: 0.4795 (mmt) cc_final: 0.4582 (mmt) REVERT: B 1126 ARG cc_start: 0.7101 (ttp-110) cc_final: 0.6569 (ttp-110) REVERT: C 76 MET cc_start: 0.7071 (mmm) cc_final: 0.6330 (mmm) REVERT: C 271 GLU cc_start: 0.6670 (pm20) cc_final: 0.6297 (pp20) REVERT: C 272 ILE cc_start: 0.6394 (mp) cc_final: 0.6128 (mt) REVERT: C 477 LYS cc_start: 0.8129 (mttp) cc_final: 0.7853 (mttp) REVERT: C 747 PHE cc_start: 0.5040 (m-80) cc_final: 0.4779 (m-80) REVERT: C 755 PHE cc_start: 0.3627 (m-80) cc_final: 0.3118 (m-80) REVERT: C 932 MET cc_start: 0.8064 (mmt) cc_final: 0.7570 (mmp) REVERT: C 934 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.5671 (mmt) REVERT: C 1083 PHE cc_start: 0.6042 (t80) cc_final: 0.5496 (t80) REVERT: C 1084 MET cc_start: 0.4818 (mmt) cc_final: 0.4606 (mmt) REVERT: C 1126 ARG cc_start: 0.7093 (ttp-110) cc_final: 0.6560 (ttp-110) REVERT: D 76 MET cc_start: 0.7044 (mmm) cc_final: 0.6305 (mmm) REVERT: D 271 GLU cc_start: 0.6666 (pm20) cc_final: 0.6295 (pp20) REVERT: D 272 ILE cc_start: 0.6403 (mp) cc_final: 0.6136 (mt) REVERT: D 572 PHE cc_start: 0.6561 (t80) cc_final: 0.6057 (t80) REVERT: D 592 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6393 (tm130) REVERT: D 747 PHE cc_start: 0.5042 (m-80) cc_final: 0.4780 (m-80) REVERT: D 755 PHE cc_start: 0.3637 (m-80) cc_final: 0.3120 (m-80) REVERT: D 932 MET cc_start: 0.8072 (mmt) cc_final: 0.7579 (mmp) REVERT: D 934 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.5647 (mmt) REVERT: D 1083 PHE cc_start: 0.6035 (t80) cc_final: 0.5489 (t80) REVERT: D 1084 MET cc_start: 0.4807 (mmt) cc_final: 0.4598 (mmt) REVERT: D 1126 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6550 (ttp-110) REVERT: D 1155 GLU cc_start: 0.7932 (tp30) cc_final: 0.7692 (tp30) REVERT: D 1157 MET cc_start: 0.8147 (mmp) cc_final: 0.7858 (mmp) outliers start: 34 outliers final: 16 residues processed: 294 average time/residue: 0.2034 time to fit residues: 102.4961 Evaluate side-chains 285 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 263 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 934 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 934 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 934 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 110 optimal weight: 5.9990 chunk 531 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 363 optimal weight: 0.9990 chunk 334 optimal weight: 0.6980 chunk 157 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 509 optimal weight: 1.9990 chunk 512 optimal weight: 0.7980 chunk 436 optimal weight: 6.9990 chunk 419 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 702 ASN A1140 ASN B1140 ASN C1140 ASN D 702 ASN D1140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.086244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.070476 restraints weight = 129031.121| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.16 r_work: 0.3244 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 40927 Z= 0.101 Angle : 0.455 6.409 55945 Z= 0.231 Chirality : 0.037 0.136 6560 Planarity : 0.003 0.054 7080 Dihedral : 6.517 131.827 6716 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.41 % Allowed : 7.79 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.75 (0.11), residues: 5424 helix: 2.27 (0.09), residues: 3048 sheet: -0.83 (0.23), residues: 428 loop : -0.11 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 112 TYR 0.012 0.001 TYR D1063 PHE 0.017 0.001 PHE A1160 TRP 0.009 0.001 TRP C 620 HIS 0.002 0.001 HIS B 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (40924) covalent geometry : angle 0.45521 / 0.23 (55928) SS BOND : bond 0.00041 / 0.02 ( 3) SS BOND : angle 0.10695 / 0.07 ( 17) hydrogen bonds : bond 0.03494 / 2.40 ( 2327) hydrogen bonds : angle 3.62129 / 2.65 ( 6837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 275 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.7010 (mmm) cc_final: 0.6352 (mmm) REVERT: A 271 GLU cc_start: 0.6658 (pm20) cc_final: 0.6304 (pp20) REVERT: A 272 ILE cc_start: 0.6489 (OUTLIER) cc_final: 0.6230 (mt) REVERT: A 448 ASN cc_start: 0.6996 (m-40) cc_final: 0.6346 (t0) REVERT: A 560 MET cc_start: 0.8211 (mmm) cc_final: 0.7955 (mmm) REVERT: A 747 PHE cc_start: 0.5056 (m-80) cc_final: 0.4770 (m-80) REVERT: A 932 MET cc_start: 0.8056 (mmt) cc_final: 0.7565 (mmp) REVERT: A 934 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.5858 (mmt) REVERT: A 1083 PHE cc_start: 0.6090 (t80) cc_final: 0.5579 (t80) REVERT: A 1126 ARG cc_start: 0.7143 (ttp-110) cc_final: 0.6591 (ttp-110) REVERT: B 76 MET cc_start: 0.6999 (mmm) cc_final: 0.6329 (mmm) REVERT: B 271 GLU cc_start: 0.6673 (pm20) cc_final: 0.6308 (pp20) REVERT: B 272 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.6237 (mt) REVERT: B 448 ASN cc_start: 0.6973 (m-40) cc_final: 0.6396 (t0) REVERT: B 477 LYS cc_start: 0.8164 (mttp) cc_final: 0.7848 (mttp) REVERT: B 747 PHE cc_start: 0.5065 (m-80) cc_final: 0.4770 (m-80) REVERT: B 932 MET cc_start: 0.8044 (mmt) cc_final: 0.7549 (mmp) REVERT: B 934 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.5863 (mmt) REVERT: B 1083 PHE cc_start: 0.6092 (t80) cc_final: 0.5584 (t80) REVERT: B 1126 ARG cc_start: 0.7152 (ttp-110) cc_final: 0.6601 (ttp-110) REVERT: C 76 MET cc_start: 0.6998 (mmm) cc_final: 0.6325 (mmm) REVERT: C 271 GLU cc_start: 0.6658 (pm20) cc_final: 0.6297 (pp20) REVERT: C 272 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6231 (mt) REVERT: C 448 ASN cc_start: 0.6982 (m-40) cc_final: 0.6404 (t0) REVERT: C 477 LYS cc_start: 0.8167 (mttp) cc_final: 0.7850 (mttp) REVERT: C 747 PHE cc_start: 0.5057 (m-80) cc_final: 0.4773 (m-80) REVERT: C 932 MET cc_start: 0.8058 (mmt) cc_final: 0.7569 (mmp) REVERT: C 934 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.5863 (mmt) REVERT: C 1083 PHE cc_start: 0.6095 (t80) cc_final: 0.5587 (t80) REVERT: C 1126 ARG cc_start: 0.7144 (ttp-110) cc_final: 0.6588 (ttp-110) REVERT: D 76 MET cc_start: 0.6986 (mmm) cc_final: 0.6326 (mmm) REVERT: D 271 GLU cc_start: 0.6655 (pm20) cc_final: 0.6299 (pp20) REVERT: D 272 ILE cc_start: 0.6500 (OUTLIER) cc_final: 0.6241 (mt) REVERT: D 448 ASN cc_start: 0.6982 (m-40) cc_final: 0.6328 (t0) REVERT: D 572 PHE cc_start: 0.6415 (t80) cc_final: 0.6124 (t80) REVERT: D 592 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6517 (tp40) REVERT: D 747 PHE cc_start: 0.5083 (m-80) cc_final: 0.4795 (m-80) REVERT: D 932 MET cc_start: 0.8059 (mmt) cc_final: 0.7570 (mmp) REVERT: D 934 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.5854 (mmt) REVERT: D 1083 PHE cc_start: 0.6094 (t80) cc_final: 0.5584 (t80) REVERT: D 1126 ARG cc_start: 0.7151 (ttp-110) cc_final: 0.6595 (ttp-110) outliers start: 49 outliers final: 25 residues processed: 303 average time/residue: 0.1911 time to fit residues: 100.2308 Evaluate side-chains 291 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 934 MET Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 934 MET Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 592 GLN Chi-restraints excluded: chain D residue 699 ASN Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 934 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 148 optimal weight: 9.9990 chunk 418 optimal weight: 20.0000 chunk 424 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 510 optimal weight: 0.7980 chunk 503 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 903 HIS B1326 ASN C1326 ASN D1326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.086123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.066566 restraints weight = 126871.571| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.07 r_work: 0.3243 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40927 Z= 0.127 Angle : 0.488 6.516 55945 Z= 0.247 Chirality : 0.038 0.140 6560 Planarity : 0.004 0.053 7080 Dihedral : 6.650 133.340 6716 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.01 % Allowed : 7.84 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.70 (0.11), residues: 5424 helix: 2.25 (0.09), residues: 3024 sheet: -0.90 (0.24), residues: 428 loop : -0.13 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 612 TYR 0.013 0.001 TYR B 917 PHE 0.018 0.002 PHE D1160 TRP 0.011 0.001 TRP C 620 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (40924) covalent geometry : angle 0.48780 / 0.25 (55928) SS BOND : bond 0.00054 / 0.02 ( 3) SS BOND : angle 0.08543 / 0.05 ( 17) hydrogen bonds : bond 0.03773 / 2.60 ( 2327) hydrogen bonds : angle 3.68688 / 2.70 ( 6837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 251 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.6953 (mmm) cc_final: 0.6388 (mmm) REVERT: A 448 ASN cc_start: 0.6920 (m-40) cc_final: 0.6233 (t0) REVERT: A 560 MET cc_start: 0.8173 (mmm) cc_final: 0.7923 (mmm) REVERT: A 747 PHE cc_start: 0.5099 (m-80) cc_final: 0.4843 (m-80) REVERT: A 932 MET cc_start: 0.7920 (mmt) cc_final: 0.7699 (mmt) REVERT: A 934 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.5755 (mmt) REVERT: A 1083 PHE cc_start: 0.6044 (t80) cc_final: 0.5553 (t80) REVERT: A 1126 ARG cc_start: 0.6946 (ttp-110) cc_final: 0.6407 (ttp-110) REVERT: B 76 MET cc_start: 0.6962 (mmm) cc_final: 0.6396 (mmm) REVERT: B 448 ASN cc_start: 0.6935 (m-40) cc_final: 0.6249 (t0) REVERT: B 747 PHE cc_start: 0.5089 (m-80) cc_final: 0.4832 (m-80) REVERT: B 932 MET cc_start: 0.7922 (mmt) cc_final: 0.7699 (mmt) REVERT: B 934 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.5764 (mmt) REVERT: B 1083 PHE cc_start: 0.6049 (t80) cc_final: 0.5562 (t80) REVERT: B 1126 ARG cc_start: 0.6986 (ttp-110) cc_final: 0.6423 (ttp-110) REVERT: C 76 MET cc_start: 0.6969 (mmm) cc_final: 0.6396 (mmm) REVERT: C 448 ASN cc_start: 0.6933 (m-40) cc_final: 0.6242 (t0) REVERT: C 747 PHE cc_start: 0.5104 (m-80) cc_final: 0.4841 (m-80) REVERT: C 932 MET cc_start: 0.7926 (mmt) cc_final: 0.7707 (mmt) REVERT: C 934 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.5758 (mmt) REVERT: C 1083 PHE cc_start: 0.6056 (t80) cc_final: 0.5567 (t80) REVERT: C 1126 ARG cc_start: 0.6978 (ttp-110) cc_final: 0.6416 (ttp-110) REVERT: D 76 MET cc_start: 0.6955 (mmm) cc_final: 0.6390 (mmm) REVERT: D 448 ASN cc_start: 0.6925 (m-40) cc_final: 0.6237 (t0) REVERT: D 572 PHE cc_start: 0.6616 (t80) cc_final: 0.6138 (t80) REVERT: D 747 PHE cc_start: 0.5109 (m-80) cc_final: 0.4850 (m-80) REVERT: D 932 MET cc_start: 0.7940 (mmt) cc_final: 0.7721 (mmt) REVERT: D 934 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.5741 (mmt) REVERT: D 1083 PHE cc_start: 0.6044 (t80) cc_final: 0.5555 (t80) REVERT: D 1126 ARG cc_start: 0.6974 (ttp-110) cc_final: 0.6413 (ttp-110) outliers start: 70 outliers final: 41 residues processed: 295 average time/residue: 0.1996 time to fit residues: 101.6977 Evaluate side-chains 293 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 934 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 931 MET Chi-restraints excluded: chain C residue 934 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 699 ASN Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 931 MET Chi-restraints excluded: chain D residue 934 MET Chi-restraints excluded: chain D residue 1011 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 316 optimal weight: 6.9990 chunk 391 optimal weight: 20.0000 chunk 490 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 528 optimal weight: 0.0050 chunk 335 optimal weight: 0.8980 chunk 508 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 418 optimal weight: 0.0980 chunk 475 optimal weight: 3.9990 chunk 448 optimal weight: 8.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.086874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.067440 restraints weight = 127151.999| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.06 r_work: 0.3271 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 40927 Z= 0.090 Angle : 0.443 6.230 55945 Z= 0.223 Chirality : 0.036 0.137 6560 Planarity : 0.003 0.052 7080 Dihedral : 6.397 131.526 6716 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.38 % Allowed : 9.31 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.89 (0.11), residues: 5424 helix: 2.41 (0.09), residues: 3044 sheet: -0.87 (0.23), residues: 428 loop : -0.06 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.011 0.001 TYR B1057 PHE 0.009 0.001 PHE C 736 TRP 0.010 0.001 TRP B 620 HIS 0.002 0.000 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (40924) covalent geometry : angle 0.44288 / 0.22 (55928) SS BOND : bond 0.00025 / 0.01 ( 3) SS BOND : angle 0.13089 / 0.08 ( 17) hydrogen bonds : bond 0.03245 / 2.23 ( 2327) hydrogen bonds : angle 3.49109 / 2.55 ( 6837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.6961 (mmm) cc_final: 0.6402 (mmm) REVERT: A 448 ASN cc_start: 0.6904 (m-40) cc_final: 0.6232 (t0) REVERT: A 560 MET cc_start: 0.8172 (mmm) cc_final: 0.7864 (mmm) REVERT: A 592 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6091 (tm-30) REVERT: A 747 PHE cc_start: 0.5149 (m-80) cc_final: 0.4894 (m-80) REVERT: A 932 MET cc_start: 0.7891 (mmt) cc_final: 0.7683 (mmt) REVERT: A 1083 PHE cc_start: 0.6031 (t80) cc_final: 0.5581 (t80) REVERT: A 1126 ARG cc_start: 0.6987 (ttp-110) cc_final: 0.6451 (ttp-110) REVERT: B 76 MET cc_start: 0.6945 (mmm) cc_final: 0.6367 (mmm) REVERT: B 448 ASN cc_start: 0.6941 (m-40) cc_final: 0.6271 (t0) REVERT: B 560 MET cc_start: 0.8090 (mmm) cc_final: 0.7880 (mmm) REVERT: B 747 PHE cc_start: 0.5151 (m-80) cc_final: 0.4896 (m-80) REVERT: B 932 MET cc_start: 0.7886 (mmt) cc_final: 0.7675 (mmt) REVERT: B 1083 PHE cc_start: 0.6059 (t80) cc_final: 0.5619 (t80) REVERT: B 1126 ARG cc_start: 0.6982 (ttp-110) cc_final: 0.6443 (ttp-110) REVERT: C 76 MET cc_start: 0.6963 (mmm) cc_final: 0.6389 (mmm) REVERT: C 448 ASN cc_start: 0.6941 (m-40) cc_final: 0.6272 (t0) REVERT: C 747 PHE cc_start: 0.5099 (m-80) cc_final: 0.4835 (m-80) REVERT: C 932 MET cc_start: 0.7898 (mmt) cc_final: 0.7692 (mmt) REVERT: C 1083 PHE cc_start: 0.6063 (t80) cc_final: 0.5622 (t80) REVERT: C 1126 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6456 (ttp-110) REVERT: D 76 MET cc_start: 0.6978 (mmm) cc_final: 0.6425 (mmm) REVERT: D 448 ASN cc_start: 0.6909 (m-40) cc_final: 0.6237 (t0) REVERT: D 572 PHE cc_start: 0.6557 (t80) cc_final: 0.6147 (t80) REVERT: D 747 PHE cc_start: 0.5173 (m-80) cc_final: 0.4915 (m-80) REVERT: D 932 MET cc_start: 0.7919 (mmt) cc_final: 0.7714 (mmt) REVERT: D 1083 PHE cc_start: 0.6034 (t80) cc_final: 0.5585 (t80) REVERT: D 1126 ARG cc_start: 0.6981 (ttp-110) cc_final: 0.6444 (ttp-110) outliers start: 48 outliers final: 32 residues processed: 286 average time/residue: 0.2070 time to fit residues: 103.6590 Evaluate side-chains 283 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 931 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 699 ASN Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 931 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1160 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 4 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 477 optimal weight: 0.0370 chunk 55 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 416 optimal weight: 10.0000 chunk 309 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 overall best weight: 2.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 GLN B 562 GLN C 562 GLN D 562 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.085773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065972 restraints weight = 126921.019| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.27 r_work: 0.3214 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40927 Z= 0.164 Angle : 0.525 7.107 55945 Z= 0.265 Chirality : 0.039 0.148 6560 Planarity : 0.004 0.052 7080 Dihedral : 6.827 135.181 6716 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.44 % Allowed : 9.08 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.60 (0.11), residues: 5424 helix: 2.13 (0.09), residues: 3048 sheet: -0.97 (0.24), residues: 404 loop : -0.13 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 612 TYR 0.017 0.002 TYR B 917 PHE 0.017 0.002 PHE B 879 TRP 0.012 0.001 TRP D 620 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (40924) covalent geometry : angle 0.52556 / 0.27 (55928) SS BOND : bond 0.00098 / 0.04 ( 3) SS BOND : angle 0.13283 / 0.08 ( 17) hydrogen bonds : bond 0.04034 / 2.78 ( 2327) hydrogen bonds : angle 3.77458 / 2.76 ( 6837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 1.498 Fit side-chains REVERT: A 76 MET cc_start: 0.6909 (mmm) cc_final: 0.6411 (mmm) REVERT: A 687 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8304 (ttp) REVERT: A 1083 PHE cc_start: 0.6042 (t80) cc_final: 0.5581 (t80) REVERT: A 1126 ARG cc_start: 0.7001 (ttp-110) cc_final: 0.6443 (ttp-110) REVERT: B 76 MET cc_start: 0.6878 (mmm) cc_final: 0.6373 (mmm) REVERT: B 1083 PHE cc_start: 0.6035 (t80) cc_final: 0.5571 (t80) REVERT: B 1126 ARG cc_start: 0.7021 (ttp-110) cc_final: 0.6460 (ttp-110) REVERT: C 76 MET cc_start: 0.6884 (mmm) cc_final: 0.6376 (mmm) REVERT: C 687 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8329 (ttp) REVERT: C 1083 PHE cc_start: 0.6040 (t80) cc_final: 0.5576 (t80) REVERT: C 1126 ARG cc_start: 0.7020 (ttp-110) cc_final: 0.6466 (ttp-110) REVERT: D 76 MET cc_start: 0.6907 (mmm) cc_final: 0.6410 (mmm) REVERT: D 572 PHE cc_start: 0.6754 (t80) cc_final: 0.6234 (t80) REVERT: D 687 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8291 (ttp) REVERT: D 1083 PHE cc_start: 0.6042 (t80) cc_final: 0.5585 (t80) REVERT: D 1126 ARG cc_start: 0.7010 (ttp-110) cc_final: 0.6456 (ttp-110) REVERT: D 1150 MET cc_start: 0.8081 (mtp) cc_final: 0.7744 (mtt) outliers start: 50 outliers final: 32 residues processed: 288 average time/residue: 0.2055 time to fit residues: 103.2351 Evaluate side-chains 276 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 699 ASN Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1160 PHE Chi-restraints excluded: chain D residue 1392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 251 optimal weight: 40.0000 chunk 94 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 496 optimal weight: 0.3980 chunk 131 optimal weight: 9.9990 chunk 42 optimal weight: 0.0060 chunk 362 optimal weight: 5.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.086391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.066745 restraints weight = 126720.344| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.07 r_work: 0.3247 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 40927 Z= 0.105 Angle : 0.465 7.078 55945 Z= 0.233 Chirality : 0.037 0.136 6560 Planarity : 0.003 0.051 7080 Dihedral : 6.575 133.867 6716 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.38 % Allowed : 9.08 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.73 (0.11), residues: 5424 helix: 2.25 (0.09), residues: 3056 sheet: -1.11 (0.26), residues: 364 loop : -0.09 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 612 TYR 0.012 0.001 TYR C1057 PHE 0.014 0.001 PHE C 695 TRP 0.014 0.001 TRP C 620 HIS 0.003 0.001 HIS B1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (40924) covalent geometry : angle 0.46509 / 0.23 (55928) SS BOND : bond 0.00032 / 0.01 ( 3) SS BOND : angle 0.14994 / 0.09 ( 17) hydrogen bonds : bond 0.03482 / 2.40 ( 2327) hydrogen bonds : angle 3.57341 / 2.62 ( 6837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.6984 (mmm) cc_final: 0.6431 (mmm) REVERT: A 448 ASN cc_start: 0.6880 (m-40) cc_final: 0.6199 (t0) REVERT: A 687 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8270 (ttp) REVERT: A 931 MET cc_start: 0.8096 (ttm) cc_final: 0.7786 (mtm) REVERT: A 1083 PHE cc_start: 0.6067 (t80) cc_final: 0.5639 (t80) REVERT: A 1126 ARG cc_start: 0.6958 (ttp-110) cc_final: 0.6416 (ttp-110) REVERT: B 76 MET cc_start: 0.6914 (mmm) cc_final: 0.6446 (mmm) REVERT: B 448 ASN cc_start: 0.6905 (m-40) cc_final: 0.6262 (t0) REVERT: B 931 MET cc_start: 0.8094 (ttm) cc_final: 0.7780 (mtm) REVERT: B 1083 PHE cc_start: 0.6029 (t80) cc_final: 0.5589 (t80) REVERT: B 1126 ARG cc_start: 0.6951 (ttp-110) cc_final: 0.6408 (ttp-110) REVERT: C 76 MET cc_start: 0.6922 (mmm) cc_final: 0.6452 (mmm) REVERT: C 448 ASN cc_start: 0.6902 (m-40) cc_final: 0.6259 (t0) REVERT: C 687 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8312 (ttp) REVERT: C 931 MET cc_start: 0.8098 (ttm) cc_final: 0.7786 (mtm) REVERT: C 1083 PHE cc_start: 0.6030 (t80) cc_final: 0.5588 (t80) REVERT: C 1126 ARG cc_start: 0.6957 (ttp-110) cc_final: 0.6417 (ttp-110) REVERT: D 76 MET cc_start: 0.6985 (mmm) cc_final: 0.6430 (mmm) REVERT: D 448 ASN cc_start: 0.6850 (m-40) cc_final: 0.6193 (t0) REVERT: D 572 PHE cc_start: 0.6585 (t80) cc_final: 0.6149 (t80) REVERT: D 687 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8259 (ttp) REVERT: D 931 MET cc_start: 0.8097 (ttm) cc_final: 0.7785 (mtm) REVERT: D 1083 PHE cc_start: 0.6064 (t80) cc_final: 0.5642 (t80) REVERT: D 1126 ARG cc_start: 0.6950 (ttp-110) cc_final: 0.6411 (ttp-110) outliers start: 48 outliers final: 30 residues processed: 286 average time/residue: 0.2032 time to fit residues: 101.6336 Evaluate side-chains 279 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1392 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1392 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 699 ASN Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 2 optimal weight: 0.0050 chunk 361 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 117 optimal weight: 0.0050 chunk 295 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 227 optimal weight: 0.1980 chunk 304 optimal weight: 0.9990 chunk 496 optimal weight: 0.0980 overall best weight: 0.2408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.087418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068105 restraints weight = 127730.385| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.09 r_work: 0.3286 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 40927 Z= 0.083 Angle : 0.438 7.367 55945 Z= 0.218 Chirality : 0.036 0.134 6560 Planarity : 0.003 0.051 7080 Dihedral : 6.257 130.597 6716 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.92 % Allowed : 9.48 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 2.05 (0.12), residues: 5424 helix: 2.58 (0.09), residues: 3024 sheet: -0.82 (0.24), residues: 448 loop : -0.04 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 566 TYR 0.010 0.001 TYR C1057 PHE 0.026 0.001 PHE D 75 TRP 0.015 0.001 TRP D 726 HIS 0.002 0.000 HIS C1156 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.08 (40924) covalent geometry : angle 0.43810 / 0.22 (55928) SS BOND : bond 0.00017 / 0.01 ( 3) SS BOND : angle 0.17912 / 0.11 ( 17) hydrogen bonds : bond 0.02950 / 2.02 ( 2327) hydrogen bonds : angle 3.36130 / 2.46 ( 6837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 1.135 Fit side-chains REVERT: A 76 MET cc_start: 0.6972 (mmm) cc_final: 0.6497 (mmm) REVERT: A 448 ASN cc_start: 0.6904 (m-40) cc_final: 0.6316 (t0) REVERT: A 560 MET cc_start: 0.8071 (mmm) cc_final: 0.7850 (mmm) REVERT: A 687 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8310 (ttp) REVERT: A 1083 PHE cc_start: 0.5946 (t80) cc_final: 0.5559 (t80) REVERT: A 1126 ARG cc_start: 0.6975 (ttp-110) cc_final: 0.6424 (ttp-110) REVERT: B 76 MET cc_start: 0.7023 (mmm) cc_final: 0.6540 (mmm) REVERT: B 448 ASN cc_start: 0.6918 (m-40) cc_final: 0.6335 (t0) REVERT: B 560 MET cc_start: 0.8074 (mmm) cc_final: 0.7853 (mmm) REVERT: B 1083 PHE cc_start: 0.5927 (t80) cc_final: 0.5528 (t80) REVERT: B 1126 ARG cc_start: 0.6966 (ttp-110) cc_final: 0.6419 (ttp-110) REVERT: C 76 MET cc_start: 0.7030 (mmm) cc_final: 0.6549 (mmm) REVERT: C 448 ASN cc_start: 0.6914 (m-40) cc_final: 0.6333 (t0) REVERT: C 560 MET cc_start: 0.8060 (mmm) cc_final: 0.7834 (mmm) REVERT: C 687 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8342 (ttp) REVERT: C 1083 PHE cc_start: 0.5934 (t80) cc_final: 0.5535 (t80) REVERT: C 1126 ARG cc_start: 0.6970 (ttp-110) cc_final: 0.6424 (ttp-110) REVERT: D 76 MET cc_start: 0.6987 (mmm) cc_final: 0.6513 (mmm) REVERT: D 448 ASN cc_start: 0.6907 (m-40) cc_final: 0.6319 (t0) REVERT: D 572 PHE cc_start: 0.6545 (t80) cc_final: 0.6082 (t80) REVERT: D 687 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8274 (ttp) REVERT: D 1083 PHE cc_start: 0.5946 (t80) cc_final: 0.5561 (t80) REVERT: D 1126 ARG cc_start: 0.6958 (ttp-110) cc_final: 0.6412 (ttp-110) outliers start: 32 outliers final: 24 residues processed: 288 average time/residue: 0.2025 time to fit residues: 101.6158 Evaluate side-chains 269 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1392 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1392 LEU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 699 ASN Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 32 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 446 optimal weight: 6.9990 chunk 390 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 447 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 328 optimal weight: 0.0570 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1359 GLN C1359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.085956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066355 restraints weight = 126802.669| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.08 r_work: 0.3236 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40927 Z= 0.139 Angle : 0.510 7.159 55945 Z= 0.256 Chirality : 0.039 0.141 6560 Planarity : 0.004 0.051 7080 Dihedral : 6.681 133.895 6716 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.01 % Allowed : 9.51 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 1.85 (0.11), residues: 5424 helix: 2.35 (0.09), residues: 3028 sheet: -1.02 (0.24), residues: 404 loop : 0.00 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 612 TYR 0.017 0.002 TYR B 917 PHE 0.018 0.002 PHE D 75 TRP 0.013 0.001 TRP C 620 HIS 0.005 0.001 HIS D1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (40924) covalent geometry : angle 0.51048 / 0.26 (55928) SS BOND : bond 0.00086 / 0.04 ( 3) SS BOND : angle 0.07949 / 0.05 ( 17) hydrogen bonds : bond 0.03846 / 2.65 ( 2327) hydrogen bonds : angle 3.64545 / 2.67 ( 6837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 1.576 Fit side-chains REVERT: A 76 MET cc_start: 0.7058 (mmm) cc_final: 0.6632 (mmm) REVERT: A 448 ASN cc_start: 0.6963 (m-40) cc_final: 0.6300 (t0) REVERT: A 687 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8308 (ttp) REVERT: A 1083 PHE cc_start: 0.5965 (t80) cc_final: 0.5571 (t80) REVERT: A 1126 ARG cc_start: 0.7013 (ttp-110) cc_final: 0.6483 (ttp-110) REVERT: A 1216 TRP cc_start: 0.6782 (m100) cc_final: 0.6177 (m100) REVERT: B 76 MET cc_start: 0.7031 (mmm) cc_final: 0.6624 (mmm) REVERT: B 448 ASN cc_start: 0.6980 (m-40) cc_final: 0.6323 (t0) REVERT: B 1083 PHE cc_start: 0.5979 (t80) cc_final: 0.5577 (t80) REVERT: B 1126 ARG cc_start: 0.7005 (ttp-110) cc_final: 0.6473 (ttp-110) REVERT: B 1216 TRP cc_start: 0.6792 (m100) cc_final: 0.6183 (m100) REVERT: C 76 MET cc_start: 0.7051 (mmm) cc_final: 0.6640 (mmm) REVERT: C 448 ASN cc_start: 0.6983 (m-40) cc_final: 0.6323 (t0) REVERT: C 687 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8356 (ttp) REVERT: C 1083 PHE cc_start: 0.5985 (t80) cc_final: 0.5584 (t80) REVERT: C 1126 ARG cc_start: 0.7005 (ttp-110) cc_final: 0.6477 (ttp-110) REVERT: C 1216 TRP cc_start: 0.6798 (m100) cc_final: 0.6187 (m100) REVERT: D 76 MET cc_start: 0.7061 (mmm) cc_final: 0.6637 (mmm) REVERT: D 572 PHE cc_start: 0.6564 (t80) cc_final: 0.6149 (t80) REVERT: D 687 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8312 (ttp) REVERT: D 1083 PHE cc_start: 0.5968 (t80) cc_final: 0.5577 (t80) REVERT: D 1126 ARG cc_start: 0.7006 (ttp-110) cc_final: 0.6482 (ttp-110) REVERT: D 1150 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.6758 (mpp) REVERT: D 1216 TRP cc_start: 0.6801 (m100) cc_final: 0.6205 (m100) outliers start: 35 outliers final: 27 residues processed: 276 average time/residue: 0.2163 time to fit residues: 104.3437 Evaluate side-chains 280 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 699 ASN Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1392 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 699 ASN Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1392 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 699 ASN Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1392 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 699 ASN Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1160 PHE Chi-restraints excluded: chain D residue 1392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 12 optimal weight: 1.9990 chunk 273 optimal weight: 20.0000 chunk 235 optimal weight: 0.7980 chunk 472 optimal weight: 0.0980 chunk 482 optimal weight: 0.8980 chunk 134 optimal weight: 0.3980 chunk 153 optimal weight: 8.9990 chunk 411 optimal weight: 30.0000 chunk 467 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.086619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.067157 restraints weight = 127000.703| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.07 r_work: 0.3260 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 40927 Z= 0.094 Angle : 0.458 6.817 55945 Z= 0.228 Chirality : 0.037 0.134 6560 Planarity : 0.003 0.051 7080 Dihedral : 6.415 132.401 6716 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.78 % Allowed : 9.94 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 2.00 (0.12), residues: 5424 helix: 2.52 (0.09), residues: 3024 sheet: -0.86 (0.24), residues: 448 loop : -0.01 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 566 TYR 0.011 0.001 TYR C1057 PHE 0.022 0.001 PHE A 75 TRP 0.013 0.001 TRP D 620 HIS 0.003 0.001 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (40924) covalent geometry : angle 0.45829 / 0.23 (55928) SS BOND : bond 0.00006 / 0.00 ( 3) SS BOND : angle 0.15244 / 0.09 ( 17) hydrogen bonds : bond 0.03267 / 2.25 ( 2327) hydrogen bonds : angle 3.46852 / 2.54 ( 6837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11929.79 seconds wall clock time: 203 minutes 27.71 seconds (12207.71 seconds total)