Starting phenix.real_space_refine on Fri Mar 6 08:15:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pe8_13348/03_2026/7pe8_13348.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pe8_13348/03_2026/7pe8_13348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pe8_13348/03_2026/7pe8_13348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pe8_13348/03_2026/7pe8_13348.map" model { file = "/net/cci-nas-00/data/ceres_data/7pe8_13348/03_2026/7pe8_13348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pe8_13348/03_2026/7pe8_13348.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.036 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 Zn 1 6.06 5 P 6 5.49 5 S 175 5.16 5 C 18538 2.51 5 N 5204 2.21 5 O 5367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29291 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2194, 16419 Classifications: {'peptide': 2194} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 88, 'TRANS': 2105} Chain breaks: 20 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1672 Unresolved non-hydrogen dihedrals: 1079 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'ASN:plan1': 10, 'GLN:plan1': 23, 'PHE:plan': 19, 'ARG:plan': 31, 'GLU:plan': 33, 'HIS:plan': 9, 'TYR:plan': 8, 'ASP:plan': 18, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 714 Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 8917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8917 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1077} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 2, 'GLU:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26955 SG CYS E1520 23.532 72.657 159.762 1.00 74.85 S ATOM 26981 SG CYS E1523 19.727 72.771 160.082 1.00 74.86 S ATOM 27441 SG CYS E1651 21.610 75.958 159.124 1.00 65.02 S Time building chain proxies: 5.88, per 1000 atoms: 0.20 Number of scatterers: 29291 At special positions: 0 Unit cell: (151.294, 155.526, 205.252, 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) Zn 1 29.99 S 175 16.00 P 6 15.00 O 5367 8.00 N 5204 7.00 C 18538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E4801 " pdb="ZN ZN E4801 " - pdb=" NE2 HIS E1515 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1523 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1651 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1520 " Number of angles added : 3 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7310 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 16 sheets defined 67.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 74 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.647A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.095A pdb=" N LYS A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 156 removed outlier: 4.173A pdb=" N ALA A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.571A pdb=" N PHE A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.533A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 4.089A pdb=" N GLU A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 removed outlier: 3.720A pdb=" N GLY A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 376 Processing helix chain 'A' and resid 387 through 403 removed outlier: 3.764A pdb=" N ASN A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) Proline residue: A 397 - end of helix removed outlier: 3.553A pdb=" N ALA A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.872A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 removed outlier: 3.904A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 removed outlier: 3.630A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.503A pdb=" N PHE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 removed outlier: 4.306A pdb=" N GLU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 3.738A pdb=" N ALA A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.722A pdb=" N LEU A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 590 removed outlier: 3.525A pdb=" N LEU A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 removed outlier: 3.806A pdb=" N ARG A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.891A pdb=" N ARG A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 620 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 666 removed outlier: 3.523A pdb=" N ALA A 653 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 660 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.733A pdb=" N ARG A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 686 removed outlier: 4.009A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.952A pdb=" N GLN A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 722 removed outlier: 3.574A pdb=" N ARG A 708 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A 717 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 743 removed outlier: 3.546A pdb=" N PHE A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 733 " --> pdb=" O PHE A 729 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 764 removed outlier: 3.550A pdb=" N LYS A 750 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 751 " --> pdb=" O GLY A 747 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 752 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 759 " --> pdb=" O ARG A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 removed outlier: 3.811A pdb=" N ILE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 4.130A pdb=" N ALA A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 784 " --> pdb=" O ILE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.588A pdb=" N ASN A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 797 " --> pdb=" O GLY A 793 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 829 removed outlier: 4.326A pdb=" N ILE A 822 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 Processing helix chain 'A' and resid 847 through 852 removed outlier: 3.660A pdb=" N THR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 removed outlier: 3.524A pdb=" N LYS A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 875 removed outlier: 3.897A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 892 removed outlier: 3.527A pdb=" N ARG A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.683A pdb=" N VAL A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 958 removed outlier: 3.895A pdb=" N TYR A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Proline residue: A 948 - end of helix removed outlier: 3.900A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 967 through 983 removed outlier: 3.789A pdb=" N VAL A 972 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 977 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 989 through 1004 Proline residue: A 995 - end of helix removed outlier: 3.538A pdb=" N ASN A 999 " --> pdb=" O PRO A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1023 removed outlier: 4.412A pdb=" N GLU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1042 removed outlier: 4.015A pdb=" N GLU A1040 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1064 removed outlier: 3.518A pdb=" N VAL A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1069 Processing helix chain 'A' and resid 1070 through 1080 removed outlier: 4.066A pdb=" N LEU A1074 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Proline residue: A1076 - end of helix removed outlier: 3.710A pdb=" N ARG A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 4.069A pdb=" N ALA A1099 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1123 Proline residue: A1116 - end of helix removed outlier: 3.807A pdb=" N LEU A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE A1122 " --> pdb=" O ILE A1118 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP A1123 " --> pdb=" O VAL A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1144 removed outlier: 3.804A pdb=" N VAL A1139 " --> pdb=" O ALA A1135 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A1140 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1161 removed outlier: 3.730A pdb=" N ILE A1159 " --> pdb=" O ILE A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1182 removed outlier: 4.056A pdb=" N ASP A1175 " --> pdb=" O SER A1171 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1190 removed outlier: 3.787A pdb=" N TYR A1188 " --> pdb=" O GLY A1185 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1203 removed outlier: 3.841A pdb=" N LYS A1197 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL A1198 " --> pdb=" O MET A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1218 Processing helix chain 'A' and resid 1228 through 1238 Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 3.860A pdb=" N ALA A1268 " --> pdb=" O ASN A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1294 removed outlier: 3.559A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.792A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 removed outlier: 3.555A pdb=" N ARG A1315 " --> pdb=" O ASN A1311 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1311 through 1316' Processing helix chain 'A' and resid 1317 through 1329 removed outlier: 3.611A pdb=" N SER A1324 " --> pdb=" O ALA A1320 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1346 removed outlier: 3.798A pdb=" N GLU A1336 " --> pdb=" O ASP A1332 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1337 " --> pdb=" O GLN A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1367 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1379 through 1387 Processing helix chain 'A' and resid 1392 through 1407 removed outlier: 3.513A pdb=" N HIS A1398 " --> pdb=" O ALA A1394 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A1407 " --> pdb=" O GLU A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1422 Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.536A pdb=" N VAL A1432 " --> pdb=" O ALA A1428 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A1433 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 4.299A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A1453 " --> pdb=" O TRP A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1469 removed outlier: 3.970A pdb=" N VAL A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A1462 " --> pdb=" O ASP A1458 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A1469 " --> pdb=" O LYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 removed outlier: 3.737A pdb=" N ALA A1486 " --> pdb=" O ARG A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1501 removed outlier: 3.679A pdb=" N GLN A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1524 removed outlier: 4.047A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A1512 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1534 removed outlier: 3.764A pdb=" N GLU A1530 " --> pdb=" O TRP A1526 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 removed outlier: 4.073A pdb=" N ARG A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1550 " --> pdb=" O TYR A1546 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A1554 " --> pdb=" O LEU A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1580 removed outlier: 3.631A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A1569 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A1570 " --> pdb=" O LYS A1566 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A1578 " --> pdb=" O GLU A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1588 removed outlier: 3.596A pdb=" N TYR A1587 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY A1588 " --> pdb=" O ARG A1585 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1584 through 1588' Processing helix chain 'A' and resid 1589 through 1608 removed outlier: 3.727A pdb=" N GLU A1600 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A1601 " --> pdb=" O SER A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1612 Processing helix chain 'A' and resid 1614 through 1626 removed outlier: 5.422A pdb=" N TRP A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A1623 " --> pdb=" O TRP A1619 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A1625 " --> pdb=" O GLU A1621 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1640 Processing helix chain 'A' and resid 1645 through 1648 Processing helix chain 'A' and resid 1649 through 1664 removed outlier: 4.008A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A1655 " --> pdb=" O ARG A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 removed outlier: 3.527A pdb=" N ALA A1669 " --> pdb=" O ARG A1665 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A1676 " --> pdb=" O THR A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1708 Processing helix chain 'A' and resid 1711 through 1729 removed outlier: 3.569A pdb=" N GLN A1725 " --> pdb=" O VAL A1721 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A1726 " --> pdb=" O GLN A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1762 removed outlier: 3.552A pdb=" N ARG A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1783 removed outlier: 3.510A pdb=" N ASP A1783 " --> pdb=" O ALA A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1809 removed outlier: 3.591A pdb=" N ALA A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1802 " --> pdb=" O PHE A1798 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A1809 " --> pdb=" O LYS A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1874 through 1896 removed outlier: 4.227A pdb=" N MET A1879 " --> pdb=" O LYS A1875 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR A1880 " --> pdb=" O THR A1876 " (cutoff:3.500A) Proline residue: A1883 - end of helix removed outlier: 3.541A pdb=" N SER A1893 " --> pdb=" O PHE A1889 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A1894 " --> pdb=" O ARG A1890 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A1896 " --> pdb=" O ILE A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1914 removed outlier: 4.053A pdb=" N LEU A1907 " --> pdb=" O THR A1903 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A1908 " --> pdb=" O LEU A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1916 through 1930 removed outlier: 3.539A pdb=" N GLU A1921 " --> pdb=" O PRO A1917 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A1922 " --> pdb=" O ASP A1918 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A1925 " --> pdb=" O GLU A1921 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A1928 " --> pdb=" O VAL A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1944 Processing helix chain 'A' and resid 1950 through 1968 removed outlier: 4.561A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A1957 " --> pdb=" O VAL A1953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1981 removed outlier: 3.955A pdb=" N LEU A1972 " --> pdb=" O HIS A1968 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TYR A1974 " --> pdb=" O GLN A1970 " (cutoff:3.500A) Proline residue: A1975 - end of helix Processing helix chain 'A' and resid 1984 through 1999 Processing helix chain 'A' and resid 2002 through 2021 removed outlier: 4.440A pdb=" N VAL A2006 " --> pdb=" O SER A2002 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2040 Processing helix chain 'A' and resid 2044 through 2059 removed outlier: 3.747A pdb=" N VAL A2050 " --> pdb=" O GLY A2046 " (cutoff:3.500A) Proline residue: A2053 - end of helix removed outlier: 3.833A pdb=" N MET A2058 " --> pdb=" O LEU A2054 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A2059 " --> pdb=" O HIS A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2064 through 2074 Processing helix chain 'A' and resid 2074 through 2092 removed outlier: 3.526A pdb=" N MET A2089 " --> pdb=" O CYS A2085 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2113 removed outlier: 3.797A pdb=" N LEU A2097 " --> pdb=" O ASN A2093 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A2103 " --> pdb=" O GLN A2099 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2192 through 2211 Processing helix chain 'A' and resid 2212 through 2217 removed outlier: 3.652A pdb=" N ARG A2217 " --> pdb=" O PRO A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2257 removed outlier: 3.516A pdb=" N TYR A2253 " --> pdb=" O LEU A2249 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2279 through 2294 removed outlier: 3.638A pdb=" N GLU A2285 " --> pdb=" O MET A2281 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2306 removed outlier: 3.716A pdb=" N TRP A2304 " --> pdb=" O ALA A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2335 removed outlier: 3.521A pdb=" N ALA A2325 " --> pdb=" O THR A2321 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A2326 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A2327 " --> pdb=" O SER A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2340 through 2342 No H-bonds generated for 'chain 'A' and resid 2340 through 2342' Processing helix chain 'A' and resid 2363 through 2368 removed outlier: 3.752A pdb=" N THR A2367 " --> pdb=" O GLU A2363 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A2368 " --> pdb=" O VAL A2364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2363 through 2368' Processing helix chain 'A' and resid 2380 through 2385 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2410 through 2423 removed outlier: 3.760A pdb=" N VAL A2417 " --> pdb=" O SER A2413 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2508 Processing helix chain 'A' and resid 2520 through 2534 Processing helix chain 'A' and resid 2534 through 2540 removed outlier: 3.915A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'E' and resid 32 through 43 removed outlier: 3.947A pdb=" N ARG E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 52 through 70 Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.547A pdb=" N ILE E 84 " --> pdb=" O HIS E 80 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 113 through 123 Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.596A pdb=" N ARG E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 157 Processing helix chain 'E' and resid 158 through 161 removed outlier: 3.864A pdb=" N PHE E 161 " --> pdb=" O ALA E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 161' Processing helix chain 'E' and resid 162 through 175 removed outlier: 3.543A pdb=" N THR E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 removed outlier: 4.028A pdb=" N ILE E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.814A pdb=" N VAL E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 removed outlier: 3.660A pdb=" N THR E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 235 removed outlier: 3.693A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.655A pdb=" N ILE E 253 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 272 through 292 removed outlier: 3.534A pdb=" N ARG E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 302 removed outlier: 4.096A pdb=" N ASN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 315 removed outlier: 3.667A pdb=" N SER E 311 " --> pdb=" O SER E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 335 removed outlier: 3.547A pdb=" N GLY E 326 " --> pdb=" O GLU E 322 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 352 removed outlier: 3.550A pdb=" N ALA E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 369 through 377 removed outlier: 3.931A pdb=" N THR E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 403 removed outlier: 3.600A pdb=" N ASN E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 414 Processing helix chain 'E' and resid 416 through 435 removed outlier: 3.736A pdb=" N VAL E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 449 through 455 removed outlier: 3.663A pdb=" N ASN E 454 " --> pdb=" O PRO E 450 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 486 removed outlier: 3.567A pdb=" N ARG E 478 " --> pdb=" O ASN E 474 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE E 479 " --> pdb=" O CYS E 475 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 481 " --> pdb=" O LYS E 477 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 505 Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.830A pdb=" N LEU E 528 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 534 " --> pdb=" O ILE E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 556 removed outlier: 3.506A pdb=" N ILE E 551 " --> pdb=" O ASN E 547 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 552 " --> pdb=" O TRP E 548 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR E 553 " --> pdb=" O ASN E 549 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 582 removed outlier: 3.962A pdb=" N PHE E 580 " --> pdb=" O ARG E 576 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 615 removed outlier: 3.622A pdb=" N PHE E 611 " --> pdb=" O GLN E 607 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER E 615 " --> pdb=" O PHE E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 638 removed outlier: 4.039A pdb=" N ASP E 625 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU E 626 " --> pdb=" O TYR E 622 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 636 " --> pdb=" O GLN E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 654 Processing helix chain 'E' and resid 655 through 658 Processing helix chain 'E' and resid 659 through 668 removed outlier: 3.772A pdb=" N LEU E 666 " --> pdb=" O PHE E 662 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 667 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS E 668 " --> pdb=" O GLY E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 669 through 680 removed outlier: 3.784A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET E 675 " --> pdb=" O HIS E 671 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS E 678 " --> pdb=" O LYS E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 688 Processing helix chain 'E' and resid 695 through 703 Processing helix chain 'E' and resid 711 through 723 removed outlier: 3.946A pdb=" N VAL E 715 " --> pdb=" O GLY E 711 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 717 " --> pdb=" O ALA E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 735 Processing helix chain 'E' and resid 735 through 742 removed outlier: 3.910A pdb=" N LEU E 739 " --> pdb=" O HIS E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 751 removed outlier: 3.849A pdb=" N TRP E 750 " --> pdb=" O PHE E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 758 removed outlier: 3.619A pdb=" N THR E 757 " --> pdb=" O GLU E 753 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN E 758 " --> pdb=" O LEU E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 761 No H-bonds generated for 'chain 'E' and resid 759 through 761' Processing helix chain 'E' and resid 763 through 778 removed outlier: 3.627A pdb=" N GLU E 776 " --> pdb=" O ASP E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 780 through 791 Processing helix chain 'E' and resid 798 through 806 Processing helix chain 'E' and resid 807 through 810 Processing helix chain 'E' and resid 811 through 819 Processing helix chain 'E' and resid 823 through 834 Processing helix chain 'E' and resid 837 through 851 removed outlier: 3.744A pdb=" N ASP E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 887 removed outlier: 3.744A pdb=" N VAL E 887 " --> pdb=" O TYR E 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 889 through 899 removed outlier: 3.717A pdb=" N LEU E 895 " --> pdb=" O THR E 891 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 896 " --> pdb=" O GLY E 892 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 911 removed outlier: 3.665A pdb=" N ASN E 908 " --> pdb=" O GLU E 904 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 909 " --> pdb=" O LEU E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 934 removed outlier: 3.672A pdb=" N LYS E 921 " --> pdb=" O TRP E 917 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 923 " --> pdb=" O GLU E 919 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 929 " --> pdb=" O ALA E 925 " (cutoff:3.500A) Processing helix chain 'E' and resid 936 through 942 removed outlier: 4.420A pdb=" N LEU E 942 " --> pdb=" O TRP E 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 948 through 956 Processing helix chain 'E' and resid 961 through 976 removed outlier: 3.728A pdb=" N VAL E 969 " --> pdb=" O ARG E 965 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR E 970 " --> pdb=" O GLY E 966 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE E 975 " --> pdb=" O VAL E 971 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 976 " --> pdb=" O LEU E 972 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 988 removed outlier: 3.661A pdb=" N HIS E 988 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 1432 through 1436 Processing helix chain 'E' and resid 1480 through 1487 removed outlier: 3.598A pdb=" N GLN E1485 " --> pdb=" O HIS E1481 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN E1486 " --> pdb=" O LEU E1482 " (cutoff:3.500A) Processing helix chain 'E' and resid 1488 through 1494 removed outlier: 3.811A pdb=" N MET E1493 " --> pdb=" O LEU E1489 " (cutoff:3.500A) Processing helix chain 'E' and resid 1522 through 1526 Processing helix chain 'E' and resid 1609 through 1623 removed outlier: 3.737A pdb=" N LYS E1614 " --> pdb=" O ILE E1610 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E1615 " --> pdb=" O LEU E1611 " (cutoff:3.500A) Processing helix chain 'E' and resid 1628 through 1643 removed outlier: 3.804A pdb=" N ILE E1639 " --> pdb=" O GLY E1635 " (cutoff:3.500A) Processing helix chain 'E' and resid 1649 through 1663 removed outlier: 3.589A pdb=" N SER E1661 " --> pdb=" O SER E1657 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS E1662 " --> pdb=" O HIS E1658 " (cutoff:3.500A) Processing helix chain 'E' and resid 1666 through 1673 Processing helix chain 'E' and resid 1682 through 1694 removed outlier: 3.573A pdb=" N HIS E1686 " --> pdb=" O PHE E1682 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E1691 " --> pdb=" O GLU E1687 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 21 removed outlier: 3.595A pdb=" N ALA G 12 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 85 through 99 removed outlier: 4.221A pdb=" N ASN G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 removed outlier: 3.561A pdb=" N LEU G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 119 through 124' Processing helix chain 'I' and resid 315 through 321 Processing helix chain 'I' and resid 359 through 364 Processing helix chain 'I' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 3.840A pdb=" N GLN A2161 " --> pdb=" O LYS A2171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.804A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2184 through 2188 removed outlier: 3.522A pdb=" N LYS A2187 " --> pdb=" O GLY A2235 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A2235 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2243 through 2245 removed outlier: 3.621A pdb=" N ASP A2244 " --> pdb=" O LEU A2346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 39 removed outlier: 6.748A pdb=" N PHE C 26 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR C 37 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 24 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C 321 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C 317 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 50 removed outlier: 4.061A pdb=" N ALA C 47 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 60 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 81 Processing sheet with id=AA8, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.898A pdb=" N GLY C 103 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL C 91 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR C 101 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE C 93 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TRP C 99 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 removed outlier: 3.757A pdb=" N CYS C 133 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 173 through 178 removed outlier: 3.874A pdb=" N SER C 175 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS C 194 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 216 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN C 198 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 223 through 228 removed outlier: 4.013A pdb=" N GLN C 225 " --> pdb=" O CYS C 238 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 245 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 239 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.587A pdb=" N GLY C 275 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 289 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 990 through 992 Processing sheet with id=AB5, first strand: chain 'I' and resid 329 through 333 Processing sheet with id=AB6, first strand: chain 'I' and resid 342 through 344 removed outlier: 6.620A pdb=" N VAL I 343 " --> pdb=" O GLN I 353 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 374 through 375 1509 hydrogen bonds defined for protein. 4428 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: 6.18 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9837 1.34 - 1.46: 6307 1.46 - 1.58: 13406 1.58 - 1.70: 6 1.70 - 1.81: 273 Bond restraints: 29829 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.599 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.602 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C5 IHP A2601 " pdb=" O15 IHP A2601 " ideal model delta sigma weight residual 1.389 1.444 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" O15 IHP A2601 " pdb=" P5 IHP A2601 " ideal model delta sigma weight residual 1.675 1.622 0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C1 IHP A2601 " pdb=" O11 IHP A2601 " ideal model delta sigma weight residual 1.392 1.444 -0.052 2.00e-02 2.50e+03 6.80e+00 ... (remaining 29824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 40197 1.87 - 3.75: 244 3.75 - 5.62: 45 5.62 - 7.50: 8 7.50 - 9.37: 2 Bond angle restraints: 40496 Sorted by residual: angle pdb=" N ILE C 260 " pdb=" CA ILE C 260 " pdb=" C ILE C 260 " ideal model delta sigma weight residual 112.43 108.96 3.47 9.20e-01 1.18e+00 1.42e+01 angle pdb=" CA LEU E 851 " pdb=" CB LEU E 851 " pdb=" CG LEU E 851 " ideal model delta sigma weight residual 116.30 125.67 -9.37 3.50e+00 8.16e-02 7.17e+00 angle pdb=" C4 IHP A2601 " pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 120.75 128.61 -7.86 3.00e+00 1.11e-01 6.87e+00 angle pdb=" N ILE E1673 " pdb=" CA ILE E1673 " pdb=" C ILE E1673 " ideal model delta sigma weight residual 110.05 107.22 2.83 1.09e+00 8.42e-01 6.76e+00 angle pdb=" C CYS A2133 " pdb=" N ARG A2134 " pdb=" CA ARG A2134 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.48e+00 ... (remaining 40491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 17398 17.97 - 35.94: 567 35.94 - 53.91: 71 53.91 - 71.88: 6 71.88 - 89.85: 5 Dihedral angle restraints: 18047 sinusoidal: 6842 harmonic: 11205 Sorted by residual: dihedral pdb=" CA ARG A1616 " pdb=" C ARG A1616 " pdb=" N GLN A1617 " pdb=" CA GLN A1617 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA TRP E 557 " pdb=" C TRP E 557 " pdb=" N PRO E 558 " pdb=" CA PRO E 558 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TYR E 835 " pdb=" C TYR E 835 " pdb=" N ASN E 836 " pdb=" CA ASN E 836 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 18044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4147 0.056 - 0.112: 524 0.112 - 0.167: 27 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 4700 Sorted by residual: chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.59 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.59 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C5 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O15 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.42 -2.58 0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 4697 not shown) Planarity restraints: 5195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 461 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO E 462 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 462 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 462 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1116 " -0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A1117 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1117 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1117 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1115 " 0.023 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A1116 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A1116 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1116 " 0.019 5.00e-02 4.00e+02 ... (remaining 5192 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6482 2.78 - 3.31: 28673 3.31 - 3.84: 44489 3.84 - 4.37: 53979 4.37 - 4.90: 92525 Nonbonded interactions: 226148 Sorted by model distance: nonbonded pdb=" OG SER C 55 " pdb=" OD1 ASN C 71 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A 308 " pdb=" OG SER A1558 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A1343 " pdb=" OG SER A1347 " model vdw 2.267 3.040 nonbonded pdb=" O LEU E 700 " pdb=" OG SER E 704 " model vdw 2.278 3.040 nonbonded pdb=" OG SER C 239 " pdb=" OD1 ASP C 241 " model vdw 2.280 3.040 ... (remaining 226143 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.800 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.002 0.076 29834 Z= 0.093 Angle : 0.408 9.374 40499 Z= 0.205 Chirality : 0.037 0.279 4700 Planarity : 0.003 0.058 5195 Dihedral : 8.708 89.852 10737 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.65 % Allowed : 3.98 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3768 helix: 0.41 (0.11), residues: 2253 sheet: -0.13 (0.40), residues: 184 loop : -0.92 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1538 TYR 0.009 0.001 TYR E 835 PHE 0.007 0.001 PHE A1122 TRP 0.005 0.001 TRP E 750 HIS 0.002 0.000 HIS A2340 Details of bonding type rmsd covalent geometry : bond 0.00185 (29829) covalent geometry : angle 0.40822 (40496) hydrogen bonds : bond 0.29633 ( 1509) hydrogen bonds : angle 6.66664 ( 4428) metal coordination : bond 0.00383 ( 4) metal coordination : angle 1.07336 ( 3) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 527 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8522 (mmtt) REVERT: A 1377 ASP cc_start: 0.7312 (t70) cc_final: 0.6884 (t0) REVERT: A 1913 TYR cc_start: 0.8494 (m-80) cc_final: 0.8059 (m-80) REVERT: A 1963 ASP cc_start: 0.6390 (m-30) cc_final: 0.6177 (m-30) REVERT: C 95 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 118 ASN cc_start: 0.7619 (t0) cc_final: 0.7319 (p0) REVERT: C 184 TYR cc_start: 0.7406 (m-80) cc_final: 0.6975 (m-80) REVERT: C 209 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6435 (pp30) REVERT: E 175 ASP cc_start: 0.7430 (t0) cc_final: 0.6670 (t0) REVERT: E 357 ARG cc_start: 0.8196 (ptt-90) cc_final: 0.7989 (ptt-90) REVERT: E 576 ARG cc_start: 0.6792 (mmm160) cc_final: 0.6210 (mmm160) REVERT: E 908 ASN cc_start: 0.8416 (t0) cc_final: 0.8186 (t0) REVERT: E 1524 VAL cc_start: 0.8709 (p) cc_final: 0.8459 (m) REVERT: I 353 GLN cc_start: 0.8078 (tp40) cc_final: 0.7862 (tp40) REVERT: I 371 PHE cc_start: 0.6325 (m-80) cc_final: 0.6026 (m-80) outliers start: 49 outliers final: 16 residues processed: 567 average time/residue: 0.1989 time to fit residues: 175.1946 Evaluate side-chains 369 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 352 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1648 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 GLN A1398 HIS A1424 GLN A1726 GLN ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2106 HIS C 28 GLN C 71 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 ASN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.144271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.112832 restraints weight = 52885.500| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.19 r_work: 0.3399 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29834 Z= 0.139 Angle : 0.555 10.025 40499 Z= 0.288 Chirality : 0.040 0.167 4700 Planarity : 0.004 0.056 5195 Dihedral : 4.389 59.827 4165 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.69 % Allowed : 8.27 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3768 helix: 0.81 (0.11), residues: 2342 sheet: -0.52 (0.39), residues: 181 loop : -1.16 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 94 TYR 0.014 0.001 TYR A2542 PHE 0.013 0.001 PHE A1545 TRP 0.013 0.001 TRP C 247 HIS 0.009 0.001 HIS C 64 Details of bonding type rmsd covalent geometry : bond 0.00297 (29829) covalent geometry : angle 0.55478 (40496) hydrogen bonds : bond 0.05439 ( 1509) hydrogen bonds : angle 4.45689 ( 4428) metal coordination : bond 0.00749 ( 4) metal coordination : angle 0.54127 ( 3) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 401 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8424 (mmtt) REVERT: A 1213 ILE cc_start: 0.8593 (tt) cc_final: 0.8265 (pt) REVERT: A 1377 ASP cc_start: 0.7829 (t70) cc_final: 0.7384 (t0) REVERT: A 1481 MET cc_start: 0.8598 (mtt) cc_final: 0.8320 (mtt) REVERT: A 1539 ASP cc_start: 0.8175 (t0) cc_final: 0.7780 (t0) REVERT: A 1925 GLU cc_start: 0.8672 (pt0) cc_final: 0.8385 (pt0) REVERT: A 1963 ASP cc_start: 0.7042 (m-30) cc_final: 0.6607 (m-30) REVERT: C 56 MET cc_start: 0.8489 (ttp) cc_final: 0.8229 (ttp) REVERT: C 95 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 117 ARG cc_start: 0.5874 (tmt170) cc_final: 0.5364 (tmt170) REVERT: C 118 ASN cc_start: 0.8023 (t0) cc_final: 0.7647 (p0) REVERT: C 184 TYR cc_start: 0.7875 (m-80) cc_final: 0.7271 (m-80) REVERT: C 209 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6446 (pp30) REVERT: E 54 MET cc_start: 0.8168 (tpp) cc_final: 0.7937 (ptt) REVERT: E 576 ARG cc_start: 0.7324 (mmm160) cc_final: 0.7009 (mmm160) REVERT: E 594 ASP cc_start: 0.7845 (t0) cc_final: 0.7644 (t0) REVERT: E 1524 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8456 (m) REVERT: G 92 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7421 (mtm-85) REVERT: G 93 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8256 (tp) REVERT: I 404 MET cc_start: 0.2507 (tmm) cc_final: 0.2000 (ttt) outliers start: 50 outliers final: 29 residues processed: 438 average time/residue: 0.1864 time to fit residues: 130.7151 Evaluate side-chains 363 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 331 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1562 GLN Chi-restraints excluded: chain A residue 1644 VAL Chi-restraints excluded: chain A residue 1648 GLU Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 656 SER Chi-restraints excluded: chain E residue 663 ILE Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 749 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 217 optimal weight: 0.3980 chunk 108 optimal weight: 0.0050 chunk 86 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2515 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS G 88 GLN I 390 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.143643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.112148 restraints weight = 52936.868| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.05 r_work: 0.3395 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29834 Z= 0.129 Angle : 0.512 11.632 40499 Z= 0.263 Chirality : 0.040 0.161 4700 Planarity : 0.003 0.053 5195 Dihedral : 4.376 58.312 4161 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.29 % Allowed : 9.65 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3768 helix: 1.05 (0.11), residues: 2353 sheet: -0.44 (0.40), residues: 185 loop : -1.25 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 248 TYR 0.014 0.001 TYR E 835 PHE 0.011 0.001 PHE A1122 TRP 0.012 0.001 TRP A2429 HIS 0.008 0.001 HIS A2189 Details of bonding type rmsd covalent geometry : bond 0.00288 (29829) covalent geometry : angle 0.51152 (40496) hydrogen bonds : bond 0.04661 ( 1509) hydrogen bonds : angle 4.03088 ( 4428) metal coordination : bond 0.00340 ( 4) metal coordination : angle 0.54813 ( 3) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8429 (mmtt) REVERT: A 1213 ILE cc_start: 0.8615 (tt) cc_final: 0.8379 (pt) REVERT: A 1377 ASP cc_start: 0.7812 (t70) cc_final: 0.7311 (t0) REVERT: A 1539 ASP cc_start: 0.8155 (t0) cc_final: 0.7761 (t0) REVERT: A 1963 ASP cc_start: 0.6808 (m-30) cc_final: 0.6402 (m-30) REVERT: A 2041 GLU cc_start: 0.8493 (mp0) cc_final: 0.8224 (mp0) REVERT: C 56 MET cc_start: 0.8502 (ttp) cc_final: 0.8248 (ttp) REVERT: C 95 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7789 (tm-30) REVERT: C 117 ARG cc_start: 0.5705 (tmt170) cc_final: 0.5404 (tmt170) REVERT: C 118 ASN cc_start: 0.8026 (t0) cc_final: 0.7518 (p0) REVERT: C 184 TYR cc_start: 0.7735 (m-80) cc_final: 0.7328 (m-80) REVERT: E 178 GLN cc_start: 0.8282 (mt0) cc_final: 0.8061 (mt0) REVERT: E 576 ARG cc_start: 0.7299 (mmm160) cc_final: 0.7036 (mmm160) REVERT: E 594 ASP cc_start: 0.7758 (t0) cc_final: 0.7457 (t0) REVERT: E 908 ASN cc_start: 0.8590 (t0) cc_final: 0.8224 (t0) REVERT: E 1524 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8390 (m) REVERT: I 366 MET cc_start: 0.7024 (tpt) cc_final: 0.6648 (tpt) outliers start: 68 outliers final: 35 residues processed: 401 average time/residue: 0.1761 time to fit residues: 114.4392 Evaluate side-chains 361 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 ASP Chi-restraints excluded: chain A residue 1648 GLU Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 656 SER Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1679 ASP Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 42 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 337 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 339 optimal weight: 0.0570 chunk 369 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 375 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 309 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 HIS ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2219 ASN A2395 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN E 875 HIS G 34 HIS G 88 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.143115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111428 restraints weight = 52496.261| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.01 r_work: 0.3381 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29834 Z= 0.126 Angle : 0.497 10.158 40499 Z= 0.255 Chirality : 0.040 0.159 4700 Planarity : 0.003 0.052 5195 Dihedral : 4.244 58.778 4155 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.33 % Allowed : 10.36 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3768 helix: 1.15 (0.11), residues: 2359 sheet: -0.56 (0.40), residues: 185 loop : -1.33 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 386 TYR 0.015 0.001 TYR E 835 PHE 0.013 0.001 PHE A1122 TRP 0.014 0.001 TRP A2429 HIS 0.006 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00286 (29829) covalent geometry : angle 0.49698 (40496) hydrogen bonds : bond 0.04101 ( 1509) hydrogen bonds : angle 3.85484 ( 4428) metal coordination : bond 0.00138 ( 4) metal coordination : angle 0.92103 ( 3) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 355 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8404 (mmtt) REVERT: A 1213 ILE cc_start: 0.8632 (tt) cc_final: 0.8398 (pt) REVERT: A 1377 ASP cc_start: 0.7797 (t70) cc_final: 0.7234 (t0) REVERT: A 1539 ASP cc_start: 0.8180 (t0) cc_final: 0.7771 (t0) REVERT: A 1925 GLU cc_start: 0.8585 (pt0) cc_final: 0.8379 (pt0) REVERT: A 1963 ASP cc_start: 0.6828 (m-30) cc_final: 0.6434 (m-30) REVERT: A 2041 GLU cc_start: 0.8547 (mp0) cc_final: 0.8283 (mp0) REVERT: C 56 MET cc_start: 0.8524 (ttp) cc_final: 0.8243 (ttp) REVERT: C 95 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 117 ARG cc_start: 0.5836 (tmt170) cc_final: 0.5488 (tmt170) REVERT: C 118 ASN cc_start: 0.8035 (t0) cc_final: 0.7628 (p0) REVERT: C 184 TYR cc_start: 0.7728 (m-80) cc_final: 0.7330 (m-80) REVERT: C 209 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6518 (pp30) REVERT: C 215 LYS cc_start: 0.7253 (ttpt) cc_final: 0.6938 (mmtm) REVERT: C 248 ARG cc_start: 0.8390 (ptm160) cc_final: 0.8077 (ptm160) REVERT: E 178 GLN cc_start: 0.8339 (mt0) cc_final: 0.8092 (mt0) REVERT: E 576 ARG cc_start: 0.7259 (mmm160) cc_final: 0.6700 (mmm160) REVERT: E 594 ASP cc_start: 0.7848 (t0) cc_final: 0.7486 (t0) REVERT: E 908 ASN cc_start: 0.8612 (t0) cc_final: 0.8260 (t0) REVERT: E 1517 ASP cc_start: 0.7318 (t70) cc_final: 0.6935 (t70) REVERT: E 1524 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8393 (m) REVERT: I 329 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7704 (ttmt) REVERT: I 366 MET cc_start: 0.6958 (tpt) cc_final: 0.6718 (tpt) outliers start: 69 outliers final: 45 residues processed: 404 average time/residue: 0.1862 time to fit residues: 119.9741 Evaluate side-chains 380 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 333 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1562 GLN Chi-restraints excluded: chain A residue 1648 GLU Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2047 MET Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 637 SER Chi-restraints excluded: chain E residue 656 SER Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 749 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1679 ASP Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 257 optimal weight: 0.1980 chunk 146 optimal weight: 0.8980 chunk 368 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 331 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 300 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1348 GLN ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2219 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN E 540 HIS ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 796 HIS G 34 HIS G 88 GLN I 390 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.143422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112149 restraints weight = 52600.083| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.04 r_work: 0.3392 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29834 Z= 0.115 Angle : 0.487 9.318 40499 Z= 0.249 Chirality : 0.039 0.158 4700 Planarity : 0.003 0.051 5195 Dihedral : 4.216 57.555 4155 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.36 % Allowed : 11.00 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3768 helix: 1.26 (0.11), residues: 2358 sheet: -0.65 (0.39), residues: 185 loop : -1.36 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 94 TYR 0.016 0.001 TYR E 835 PHE 0.014 0.001 PHE A1122 TRP 0.014 0.001 TRP A2429 HIS 0.006 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00259 (29829) covalent geometry : angle 0.48705 (40496) hydrogen bonds : bond 0.03819 ( 1509) hydrogen bonds : angle 3.72173 ( 4428) metal coordination : bond 0.00138 ( 4) metal coordination : angle 0.81598 ( 3) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 341 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1018 MET cc_start: 0.8537 (mmm) cc_final: 0.8336 (mmt) REVERT: A 1539 ASP cc_start: 0.8173 (t0) cc_final: 0.7781 (t0) REVERT: A 1963 ASP cc_start: 0.6768 (m-30) cc_final: 0.6371 (m-30) REVERT: A 2041 GLU cc_start: 0.8572 (mp0) cc_final: 0.8355 (mp0) REVERT: C 56 MET cc_start: 0.8503 (ttp) cc_final: 0.8236 (ttp) REVERT: C 95 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 114 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6803 (mt) REVERT: C 117 ARG cc_start: 0.5628 (tmt170) cc_final: 0.5335 (tmt170) REVERT: C 118 ASN cc_start: 0.7999 (t0) cc_final: 0.7625 (p0) REVERT: C 137 HIS cc_start: 0.6404 (t-170) cc_final: 0.6200 (t-90) REVERT: C 147 ASP cc_start: 0.7713 (p0) cc_final: 0.7476 (p0) REVERT: C 184 TYR cc_start: 0.7710 (m-80) cc_final: 0.7367 (m-80) REVERT: C 209 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6606 (pp30) REVERT: C 215 LYS cc_start: 0.7279 (ttpt) cc_final: 0.6951 (mmtm) REVERT: E 175 ASP cc_start: 0.7790 (t0) cc_final: 0.7344 (t0) REVERT: E 594 ASP cc_start: 0.7832 (t0) cc_final: 0.7427 (t0) REVERT: E 908 ASN cc_start: 0.8592 (t0) cc_final: 0.8279 (t0) REVERT: E 1524 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8379 (m) outliers start: 70 outliers final: 46 residues processed: 393 average time/residue: 0.1900 time to fit residues: 119.2819 Evaluate side-chains 367 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 318 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1562 GLN Chi-restraints excluded: chain A residue 1648 GLU Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2047 MET Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 637 SER Chi-restraints excluded: chain E residue 656 SER Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1679 ASP Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 94 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 269 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 204 optimal weight: 0.1980 chunk 366 optimal weight: 3.9990 chunk 275 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1997 ASN ** A2055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2219 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN G 34 HIS G 88 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.142988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111719 restraints weight = 52624.655| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.08 r_work: 0.3379 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29834 Z= 0.120 Angle : 0.494 9.369 40499 Z= 0.252 Chirality : 0.039 0.158 4700 Planarity : 0.003 0.051 5195 Dihedral : 4.208 57.840 4155 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.13 % Allowed : 11.40 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3768 helix: 1.32 (0.11), residues: 2357 sheet: -0.66 (0.39), residues: 185 loop : -1.41 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1955 TYR 0.016 0.001 TYR E 835 PHE 0.013 0.001 PHE A1122 TRP 0.014 0.001 TRP A2429 HIS 0.006 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00275 (29829) covalent geometry : angle 0.49382 (40496) hydrogen bonds : bond 0.03776 ( 1509) hydrogen bonds : angle 3.68512 ( 4428) metal coordination : bond 0.00212 ( 4) metal coordination : angle 1.09517 ( 3) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 335 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1018 MET cc_start: 0.8555 (mmm) cc_final: 0.8351 (mmt) REVERT: A 1539 ASP cc_start: 0.8176 (t0) cc_final: 0.7785 (t0) REVERT: A 1650 MET cc_start: 0.8353 (mtm) cc_final: 0.8099 (mtm) REVERT: A 1766 GLU cc_start: 0.7605 (tp30) cc_final: 0.7400 (tp30) REVERT: A 1925 GLU cc_start: 0.8604 (pt0) cc_final: 0.8388 (pt0) REVERT: A 1963 ASP cc_start: 0.6795 (m-30) cc_final: 0.6395 (m-30) REVERT: A 2041 GLU cc_start: 0.8544 (mp0) cc_final: 0.8327 (mp0) REVERT: C 56 MET cc_start: 0.8511 (ttp) cc_final: 0.8225 (ttp) REVERT: C 95 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 114 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6852 (mt) REVERT: C 118 ASN cc_start: 0.7993 (t0) cc_final: 0.7442 (p0) REVERT: C 147 ASP cc_start: 0.7736 (p0) cc_final: 0.7459 (p0) REVERT: C 184 TYR cc_start: 0.7733 (m-80) cc_final: 0.7401 (m-80) REVERT: C 209 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6530 (pp30) REVERT: C 215 LYS cc_start: 0.7331 (ttpt) cc_final: 0.6986 (mmtm) REVERT: E 594 ASP cc_start: 0.7869 (t0) cc_final: 0.7451 (t0) REVERT: E 908 ASN cc_start: 0.8603 (t0) cc_final: 0.8297 (t0) REVERT: E 1517 ASP cc_start: 0.7311 (t70) cc_final: 0.6915 (t70) REVERT: E 1524 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8318 (m) REVERT: I 366 MET cc_start: 0.6700 (tpt) cc_final: 0.6412 (tpt) outliers start: 63 outliers final: 48 residues processed: 383 average time/residue: 0.1957 time to fit residues: 119.7529 Evaluate side-chains 366 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1562 GLN Chi-restraints excluded: chain A residue 1648 GLU Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2047 MET Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 637 SER Chi-restraints excluded: chain E residue 656 SER Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 1483 LEU Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 277 optimal weight: 0.1980 chunk 147 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 chunk 222 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1693 HIS A1997 ASN A2219 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS G 88 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.142858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111627 restraints weight = 52698.005| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.06 r_work: 0.3385 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29834 Z= 0.118 Angle : 0.493 9.533 40499 Z= 0.252 Chirality : 0.039 0.157 4700 Planarity : 0.003 0.050 5195 Dihedral : 4.211 57.756 4155 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.19 % Allowed : 11.91 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3768 helix: 1.35 (0.11), residues: 2365 sheet: -0.61 (0.39), residues: 183 loop : -1.43 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1955 TYR 0.015 0.001 TYR A1787 PHE 0.013 0.001 PHE A1122 TRP 0.017 0.001 TRP A2429 HIS 0.007 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00269 (29829) covalent geometry : angle 0.49304 (40496) hydrogen bonds : bond 0.03682 ( 1509) hydrogen bonds : angle 3.63120 ( 4428) metal coordination : bond 0.00171 ( 4) metal coordination : angle 0.92405 ( 3) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 330 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1018 MET cc_start: 0.8582 (mmm) cc_final: 0.8365 (mmt) REVERT: A 1539 ASP cc_start: 0.8134 (t0) cc_final: 0.7753 (t0) REVERT: A 1650 MET cc_start: 0.8352 (mtm) cc_final: 0.8105 (mtm) REVERT: A 1766 GLU cc_start: 0.7626 (tp30) cc_final: 0.7273 (tp30) REVERT: A 1963 ASP cc_start: 0.6715 (m-30) cc_final: 0.6327 (m-30) REVERT: A 2041 GLU cc_start: 0.8548 (mp0) cc_final: 0.8345 (mp0) REVERT: C 56 MET cc_start: 0.8527 (ttp) cc_final: 0.8143 (ttp) REVERT: C 95 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 114 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6858 (mt) REVERT: C 117 ARG cc_start: 0.5580 (tmt170) cc_final: 0.5265 (tmt170) REVERT: C 137 HIS cc_start: 0.6415 (t-170) cc_final: 0.6016 (t-90) REVERT: C 184 TYR cc_start: 0.7691 (m-80) cc_final: 0.7398 (m-80) REVERT: C 209 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6565 (pp30) REVERT: C 215 LYS cc_start: 0.7342 (ttpt) cc_final: 0.7076 (mmtm) REVERT: C 248 ARG cc_start: 0.8353 (ptm160) cc_final: 0.8085 (ptm160) REVERT: E 594 ASP cc_start: 0.7856 (t0) cc_final: 0.7437 (t0) REVERT: E 908 ASN cc_start: 0.8593 (t0) cc_final: 0.8296 (t0) REVERT: E 1517 ASP cc_start: 0.7258 (t70) cc_final: 0.6875 (t70) REVERT: E 1524 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8311 (m) outliers start: 65 outliers final: 47 residues processed: 379 average time/residue: 0.1825 time to fit residues: 111.6032 Evaluate side-chains 363 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1562 GLN Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2047 MET Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 637 SER Chi-restraints excluded: chain E residue 656 SER Chi-restraints excluded: chain E residue 749 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 1483 LEU Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1679 ASP Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 128 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 1 optimal weight: 40.0000 chunk 138 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 260 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1997 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.141813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.110407 restraints weight = 52770.102| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.09 r_work: 0.3363 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29834 Z= 0.142 Angle : 0.522 9.415 40499 Z= 0.267 Chirality : 0.040 0.244 4700 Planarity : 0.003 0.050 5195 Dihedral : 4.144 59.163 4150 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.09 % Allowed : 12.31 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3768 helix: 1.29 (0.11), residues: 2380 sheet: -0.65 (0.39), residues: 183 loop : -1.51 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 94 TYR 0.018 0.001 TYR A1787 PHE 0.014 0.001 PHE A1122 TRP 0.017 0.001 TRP A2429 HIS 0.006 0.001 HIS A1084 Details of bonding type rmsd covalent geometry : bond 0.00331 (29829) covalent geometry : angle 0.52193 (40496) hydrogen bonds : bond 0.04010 ( 1509) hydrogen bonds : angle 3.69869 ( 4428) metal coordination : bond 0.00207 ( 4) metal coordination : angle 1.06259 ( 3) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 323 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.2485 (ppp) cc_final: 0.0211 (mmm) REVERT: A 1180 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8707 (tt) REVERT: A 1539 ASP cc_start: 0.8163 (t0) cc_final: 0.7774 (t0) REVERT: A 1650 MET cc_start: 0.8423 (mtm) cc_final: 0.8181 (mtm) REVERT: A 1766 GLU cc_start: 0.7682 (tp30) cc_final: 0.7384 (tp30) REVERT: A 1963 ASP cc_start: 0.6808 (m-30) cc_final: 0.6427 (m-30) REVERT: A 2041 GLU cc_start: 0.8530 (mp0) cc_final: 0.8330 (mp0) REVERT: C 56 MET cc_start: 0.8517 (ttp) cc_final: 0.8265 (ttm) REVERT: C 95 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7801 (tm-30) REVERT: C 114 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6859 (mt) REVERT: C 137 HIS cc_start: 0.6431 (t-170) cc_final: 0.5976 (t-90) REVERT: C 147 ASP cc_start: 0.7826 (p0) cc_final: 0.7562 (p0) REVERT: C 184 TYR cc_start: 0.7713 (m-80) cc_final: 0.7418 (m-80) REVERT: C 209 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6605 (pp30) REVERT: C 215 LYS cc_start: 0.7380 (ttpt) cc_final: 0.7121 (mmtm) REVERT: E 43 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6875 (mp10) REVERT: E 594 ASP cc_start: 0.7926 (t0) cc_final: 0.7490 (t0) REVERT: E 908 ASN cc_start: 0.8622 (t0) cc_final: 0.8294 (t0) REVERT: E 1517 ASP cc_start: 0.7399 (t70) cc_final: 0.7039 (t70) outliers start: 62 outliers final: 45 residues processed: 370 average time/residue: 0.1845 time to fit residues: 109.9571 Evaluate side-chains 363 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 314 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1562 GLN Chi-restraints excluded: chain A residue 1747 MET Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2047 MET Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2160 LEU Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain A residue 2417 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 637 SER Chi-restraints excluded: chain E residue 656 SER Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 1483 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain I residue 314 VAL Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 350 CYS Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 130 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 346 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 143 optimal weight: 0.0970 chunk 352 optimal weight: 1.9990 chunk 174 optimal weight: 0.1980 chunk 234 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 chunk 358 optimal weight: 0.0030 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1997 ASN A2219 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112322 restraints weight = 52689.047| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.56 r_work: 0.3437 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29834 Z= 0.093 Angle : 0.486 10.807 40499 Z= 0.247 Chirality : 0.039 0.267 4700 Planarity : 0.003 0.050 5195 Dihedral : 3.967 56.590 4149 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.55 % Allowed : 13.06 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3768 helix: 1.46 (0.11), residues: 2385 sheet: -0.59 (0.39), residues: 183 loop : -1.44 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 94 TYR 0.017 0.001 TYR A1787 PHE 0.012 0.001 PHE A1122 TRP 0.038 0.001 TRP A2429 HIS 0.005 0.001 HIS G 34 Details of bonding type rmsd covalent geometry : bond 0.00199 (29829) covalent geometry : angle 0.48614 (40496) hydrogen bonds : bond 0.03084 ( 1509) hydrogen bonds : angle 3.48837 ( 4428) metal coordination : bond 0.00131 ( 4) metal coordination : angle 1.35621 ( 3) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 347 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 681 GLU cc_start: 0.8048 (pm20) cc_final: 0.7753 (pm20) REVERT: A 727 MET cc_start: 0.0071 (ptt) cc_final: -0.1038 (tpp) REVERT: A 1180 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 1213 ILE cc_start: 0.8583 (tt) cc_final: 0.8375 (pt) REVERT: A 1539 ASP cc_start: 0.8032 (t0) cc_final: 0.7664 (t0) REVERT: A 1650 MET cc_start: 0.8339 (mtm) cc_final: 0.8096 (mtm) REVERT: A 1766 GLU cc_start: 0.7509 (tp30) cc_final: 0.7208 (tp30) REVERT: A 1963 ASP cc_start: 0.6547 (m-30) cc_final: 0.6176 (m-30) REVERT: C 56 MET cc_start: 0.8444 (ttp) cc_final: 0.8216 (ttp) REVERT: C 95 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 137 HIS cc_start: 0.6440 (t-170) cc_final: 0.6222 (t-90) REVERT: C 147 ASP cc_start: 0.7713 (p0) cc_final: 0.7451 (p0) REVERT: C 184 TYR cc_start: 0.7693 (m-80) cc_final: 0.7338 (m-80) REVERT: C 209 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6535 (pp30) REVERT: E 43 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6678 (mp10) REVERT: E 594 ASP cc_start: 0.7815 (t0) cc_final: 0.7404 (t0) outliers start: 46 outliers final: 34 residues processed: 376 average time/residue: 0.1831 time to fit residues: 110.9795 Evaluate side-chains 363 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 326 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1562 GLN Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2047 MET Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2219 ASN Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 749 ASN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 1483 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 350 CYS Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 262 optimal weight: 0.7980 chunk 363 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 240 optimal weight: 0.6980 chunk 347 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 368 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1931 GLN A1997 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS E 209 ASN E 540 HIS ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112650 restraints weight = 52488.262| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.01 r_work: 0.3404 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29834 Z= 0.111 Angle : 0.511 11.218 40499 Z= 0.258 Chirality : 0.039 0.269 4700 Planarity : 0.003 0.050 5195 Dihedral : 3.967 56.892 4149 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.35 % Allowed : 13.39 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3768 helix: 1.47 (0.11), residues: 2390 sheet: -0.61 (0.39), residues: 183 loop : -1.44 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 94 TYR 0.017 0.001 TYR A1787 PHE 0.023 0.001 PHE E 79 TRP 0.037 0.001 TRP A2429 HIS 0.006 0.001 HIS G 34 Details of bonding type rmsd covalent geometry : bond 0.00254 (29829) covalent geometry : angle 0.51080 (40496) hydrogen bonds : bond 0.03361 ( 1509) hydrogen bonds : angle 3.51710 ( 4428) metal coordination : bond 0.00307 ( 4) metal coordination : angle 1.03497 ( 3) Misc. bond : bond 0.00026 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 326 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 681 GLU cc_start: 0.8063 (pm20) cc_final: 0.7762 (pm20) REVERT: A 727 MET cc_start: 0.0066 (ptt) cc_final: -0.1046 (tpp) REVERT: A 1180 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 1213 ILE cc_start: 0.8611 (tt) cc_final: 0.8384 (pt) REVERT: A 1539 ASP cc_start: 0.8113 (t0) cc_final: 0.7736 (t0) REVERT: A 1650 MET cc_start: 0.8405 (mtm) cc_final: 0.8160 (mtm) REVERT: A 1766 GLU cc_start: 0.7582 (tp30) cc_final: 0.7265 (tp30) REVERT: A 1963 ASP cc_start: 0.6716 (m-30) cc_final: 0.6333 (m-30) REVERT: C 56 MET cc_start: 0.8453 (ttp) cc_final: 0.8244 (ttp) REVERT: C 95 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7793 (tm-30) REVERT: C 137 HIS cc_start: 0.6438 (t-170) cc_final: 0.6188 (t-90) REVERT: C 147 ASP cc_start: 0.7766 (p0) cc_final: 0.7487 (p0) REVERT: C 184 TYR cc_start: 0.7721 (m-80) cc_final: 0.7367 (m-80) REVERT: C 209 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6565 (pp30) REVERT: E 43 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6830 (mp10) REVERT: E 594 ASP cc_start: 0.7945 (t0) cc_final: 0.7499 (t0) REVERT: E 1517 ASP cc_start: 0.7303 (t70) cc_final: 0.6935 (t70) outliers start: 40 outliers final: 32 residues processed: 356 average time/residue: 0.1861 time to fit residues: 107.1173 Evaluate side-chains 358 residues out of total 3383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 323 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1180 LEU Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1562 GLN Chi-restraints excluded: chain A residue 1590 MET Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2047 MET Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2151 ILE Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain E residue 749 ASN Chi-restraints excluded: chain E residue 898 VAL Chi-restraints excluded: chain E residue 1483 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 344 VAL Chi-restraints excluded: chain I residue 350 CYS Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 16 optimal weight: 0.0970 chunk 148 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 235 optimal weight: 0.4980 chunk 297 optimal weight: 0.7980 chunk 361 optimal weight: 0.5980 chunk 248 optimal weight: 0.2980 chunk 311 optimal weight: 0.4980 chunk 219 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1997 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS E 209 ASN E 540 HIS ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS G 88 GLN ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.142812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111266 restraints weight = 52905.400| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.97 r_work: 0.3410 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29834 Z= 0.101 Angle : 0.505 10.641 40499 Z= 0.255 Chirality : 0.039 0.263 4700 Planarity : 0.003 0.050 5195 Dihedral : 3.945 55.846 4147 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.38 % Allowed : 13.50 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3768 helix: 1.51 (0.11), residues: 2389 sheet: -0.56 (0.39), residues: 183 loop : -1.42 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 94 TYR 0.017 0.001 TYR A1787 PHE 0.019 0.001 PHE E 79 TRP 0.037 0.001 TRP A2429 HIS 0.006 0.001 HIS G 34 Details of bonding type rmsd covalent geometry : bond 0.00226 (29829) covalent geometry : angle 0.50508 (40496) hydrogen bonds : bond 0.03203 ( 1509) hydrogen bonds : angle 3.47158 ( 4428) metal coordination : bond 0.00214 ( 4) metal coordination : angle 0.90611 ( 3) Misc. bond : bond 0.00017 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6895.11 seconds wall clock time: 118 minutes 42.50 seconds (7122.50 seconds total)