Starting phenix.real_space_refine on Thu Mar 21 05:29:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe8_13348/03_2024/7pe8_13348_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe8_13348/03_2024/7pe8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe8_13348/03_2024/7pe8_13348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe8_13348/03_2024/7pe8_13348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe8_13348/03_2024/7pe8_13348_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pe8_13348/03_2024/7pe8_13348_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 23, 'ASP:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 33, 'ARG:plan': 31} 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: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP: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: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, '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: 14.97, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 10.87 Conformation dependent library (CDL) restraints added in 4.8 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... running ksdssp... Secondary structure from input PDB file: 199 helices and 14 sheets defined 59.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.27 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 102 through 116 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) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.853A pdb=" N MET A 125 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 155 removed outlier: 4.514A pdb=" N GLU A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.571A pdb=" N PHE A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 234 through 245 removed outlier: 3.720A pdb=" N GLY A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 363 through 375 Processing helix chain 'A' and resid 387 through 402 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 424 Processing helix chain 'A' and resid 430 through 443 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 451 through 465 removed outlier: 4.104A pdb=" N ALA A 461 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 462 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU A 463 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 479 through 490 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) Processing helix chain 'A' and resid 500 through 509 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 Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 532 through 546 Processing helix chain 'A' and resid 581 through 589 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 607 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) removed outlier: 4.080A pdb=" N ALA A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 612 No H-bonds generated for 'chain 'A' and resid 609 through 612' Processing helix chain 'A' and resid 616 through 628 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 649 through 665 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 669 through 678 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 681 through 685 removed outlier: 4.009A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 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) Processing helix chain 'A' and resid 705 through 721 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 726 through 742 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 747 through 763 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 765 through 769 Processing helix chain 'A' and resid 773 through 783 removed outlier: 4.130A pdb=" N ALA A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 808 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) Processing helix chain 'A' and resid 817 through 828 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 838 through 846 Processing helix chain 'A' and resid 848 through 851 No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 856 through 860 removed outlier: 3.682A pdb=" N LYS A 860 " --> pdb=" O PRO A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 874 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 878 through 891 removed outlier: 3.527A pdb=" N ARG A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 930 through 936 removed outlier: 3.683A pdb=" N VAL A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 957 removed outlier: 3.895A pdb=" N TYR A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Proline residue: A 948 - end of helix Processing helix chain 'A' and resid 965 through 982 removed outlier: 4.234A pdb=" N THR A 969 " --> pdb=" O HIS A 966 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 970 " --> pdb=" O HIS A 967 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 971 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 972 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 976 " --> pdb=" O GLN A 973 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 979 " --> pdb=" O THR A 976 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 982 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1003 Proline residue: A 991 - end of helix removed outlier: 4.946A pdb=" N MET A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Proline residue: A 995 - end of helix removed outlier: 4.023A pdb=" N LEU A 998 " --> pdb=" O PRO A 995 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A1001 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1022 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 1031 through 1041 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 1050 through 1063 removed outlier: 3.518A pdb=" N VAL A1061 " --> pdb=" O GLU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1081 removed outlier: 3.738A pdb=" N LEU A1071 " --> pdb=" O LYS A1068 " (cutoff:3.500A) Proline residue: A1072 - end of helix Proline residue: A1076 - end of helix removed outlier: 3.511A pdb=" N LEU A1079 " --> pdb=" O PRO A1076 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A1080 " --> pdb=" O HIS A1077 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A1081 " --> pdb=" O MET A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.852A pdb=" N ILE A1091 " --> pdb=" O PRO A1088 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL A1092 " --> pdb=" O GLY A1089 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A1098 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1122 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) Processing helix chain 'A' and resid 1129 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 1156 through 1160 Processing helix chain 'A' and resid 1170 through 1181 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 1186 through 1202 removed outlier: 3.856A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Proline residue: A1193 - end of helix removed outlier: 3.797A pdb=" N ASN A1196 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS A1197 " --> pdb=" O MET A1194 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A1200 " --> pdb=" O LYS A1197 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A1202 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1217 Processing helix chain 'A' and resid 1229 through 1237 Processing helix chain 'A' and resid 1265 through 1269 Processing helix chain 'A' and resid 1277 through 1293 removed outlier: 3.559A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1309 removed outlier: 4.076A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP A1304 " --> pdb=" O LEU A1300 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1315 Processing helix chain 'A' and resid 1318 through 1328 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 1331 through 1345 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 1351 through 1366 Processing helix chain 'A' and resid 1377 through 1386 removed outlier: 3.562A pdb=" N ILE A1380 " --> pdb=" O ASP A1377 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A1381 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A1383 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A1385 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1406 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) Processing helix chain 'A' and resid 1410 through 1422 Processing helix chain 'A' and resid 1426 through 1438 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 1447 through 1453 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 1457 through 1468 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) Processing helix chain 'A' and resid 1476 through 1487 removed outlier: 3.737A pdb=" N ALA A1486 " --> pdb=" O ARG A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1500 removed outlier: 3.679A pdb=" N GLN A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1523 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 1526 through 1535 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) removed outlier: 4.318A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 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) Processing helix chain 'A' and resid 1557 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 1585 through 1587 No H-bonds generated for 'chain 'A' and resid 1585 through 1587' Processing helix chain 'A' and resid 1590 through 1607 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 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1615 through 1625 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) Processing helix chain 'A' and resid 1630 through 1641 removed outlier: 3.867A pdb=" N SER A1641 " --> pdb=" O LEU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1648 No H-bonds generated for 'chain 'A' and resid 1646 through 1648' Processing helix chain 'A' and resid 1650 through 1663 removed outlier: 3.638A pdb=" N LYS A1655 " --> pdb=" O ARG A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1677 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 1694 through 1707 Processing helix chain 'A' and resid 1712 through 1728 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 1739 through 1761 removed outlier: 3.552A pdb=" N ARG A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1782 Processing helix chain 'A' and resid 1787 through 1808 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) Processing helix chain 'A' and resid 1874 through 1895 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) Processing helix chain 'A' and resid 1900 through 1913 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 1917 through 1929 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 1939 through 1945 removed outlier: 3.922A pdb=" N ARG A1945 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1967 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 1969 through 1980 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 1985 through 2001 removed outlier: 3.932A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS A2001 " --> pdb=" O ASN A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2020 Processing helix chain 'A' and resid 2023 through 2039 Processing helix chain 'A' and resid 2045 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 2065 through 2073 Processing helix chain 'A' and resid 2075 through 2091 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 2094 through 2112 removed outlier: 3.962A pdb=" N LEU A2103 " --> pdb=" O GLN A2099 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2126 No H-bonds generated for 'chain 'A' and resid 2123 through 2126' Processing helix chain 'A' and resid 2193 through 2210 Processing helix chain 'A' and resid 2213 through 2216 No H-bonds generated for 'chain 'A' and resid 2213 through 2216' Processing helix chain 'A' and resid 2246 through 2256 removed outlier: 3.516A pdb=" N TYR A2253 " --> pdb=" O LEU A2249 " (cutoff:3.500A) Processing helix chain 'A' and resid 2263 through 2271 Processing helix chain 'A' and resid 2280 through 2293 removed outlier: 3.638A pdb=" N GLU A2285 " --> pdb=" O MET A2281 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2306 removed outlier: 3.716A pdb=" N TRP A2304 " --> pdb=" O ALA A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2334 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 2341 through 2343 No H-bonds generated for 'chain 'A' and resid 2341 through 2343' Processing helix chain 'A' and resid 2364 through 2367 No H-bonds generated for 'chain 'A' and resid 2364 through 2367' Processing helix chain 'A' and resid 2381 through 2384 No H-bonds generated for 'chain 'A' and resid 2381 through 2384' Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2411 through 2422 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 2495 through 2509 Processing helix chain 'A' and resid 2521 through 2533 Processing helix chain 'A' and resid 2535 through 2539 Processing helix chain 'A' and resid 2543 through 2545 No H-bonds generated for 'chain 'A' and resid 2543 through 2545' Processing helix chain 'E' and resid 33 through 42 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 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 53 through 69 Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.523A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 125 through 133 removed outlier: 3.526A pdb=" N ILE E 129 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA E 130 " --> pdb=" O TYR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 156 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'E' and resid 185 through 197 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 199 through 204 Processing helix chain 'E' and resid 207 through 216 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) Processing helix chain 'E' and resid 221 through 234 removed outlier: 3.693A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 250 through 258 removed outlier: 3.655A pdb=" N ILE E 253 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Proline residue: E 256 - end of helix Processing helix chain 'E' and resid 273 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 295 through 301 removed outlier: 4.096A pdb=" N ASN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 removed outlier: 3.644A pdb=" N LEU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 334 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 346 through 352 removed outlier: 3.613A pdb=" N SER E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.931A pdb=" N THR E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 402 Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 417 through 434 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 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 450 through 454 removed outlier: 3.663A pdb=" N ASN E 454 " --> pdb=" O PRO E 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 450 through 454' Processing helix chain 'E' and resid 463 through 485 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 492 through 504 Processing helix chain 'E' and resid 525 through 535 removed outlier: 3.614A pdb=" N ASP E 534 " --> pdb=" O ILE E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 555 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 568 through 581 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 598 through 614 removed outlier: 3.622A pdb=" N PHE E 611 " --> pdb=" O GLN E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 637 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 648 through 653 Processing helix chain 'E' and resid 655 through 657 No H-bonds generated for 'chain 'E' and resid 655 through 657' Processing helix chain 'E' and resid 660 through 667 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) Processing helix chain 'E' and resid 670 through 679 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 682 through 689 removed outlier: 3.748A pdb=" N CYS E 689 " --> pdb=" O LEU E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 696 through 702 Processing helix chain 'E' and resid 712 through 722 removed outlier: 3.641A pdb=" N LEU E 717 " --> pdb=" O ALA E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 741 removed outlier: 3.530A pdb=" N LEU E 736 " --> pdb=" O ALA E 732 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG E 737 " --> pdb=" O THR E 733 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL E 738 " --> pdb=" O LYS E 734 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU E 739 " --> pdb=" O HIS E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 750 No H-bonds generated for 'chain 'E' and resid 747 through 750' Processing helix chain 'E' and resid 752 through 760 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) removed outlier: 3.835A pdb=" N LEU E 759 " --> pdb=" O LEU E 755 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS E 760 " --> pdb=" O VAL E 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 779 removed outlier: 3.627A pdb=" N GLU E 776 " --> pdb=" O ASP E 772 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 790 Processing helix chain 'E' and resid 799 through 810 removed outlier: 3.649A pdb=" N ARG E 807 " --> pdb=" O LEU E 803 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE E 808 " --> pdb=" O LEU E 804 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU E 809 " --> pdb=" O LEU E 805 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER E 810 " --> pdb=" O LEU E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 820 removed outlier: 3.562A pdb=" N GLU E 820 " --> pdb=" O SER E 816 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 833 Processing helix chain 'E' and resid 838 through 850 Processing helix chain 'E' and resid 882 through 886 Processing helix chain 'E' and resid 890 through 898 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 902 through 910 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 917 through 935 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) removed outlier: 3.687A pdb=" N SER E 935 " --> pdb=" O GLY E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 941 Processing helix chain 'E' and resid 949 through 955 Processing helix chain 'E' and resid 962 through 977 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) removed outlier: 3.876A pdb=" N LYS E 977 " --> pdb=" O GLY E 973 " (cutoff:3.500A) Processing helix chain 'E' and resid 979 through 987 Processing helix chain 'E' and resid 1433 through 1435 No H-bonds generated for 'chain 'E' and resid 1433 through 1435' Processing helix chain 'E' and resid 1480 through 1485 removed outlier: 3.598A pdb=" N GLN E1485 " --> pdb=" O HIS E1481 " (cutoff:3.500A) Processing helix chain 'E' and resid 1489 through 1493 removed outlier: 3.811A pdb=" N MET E1493 " --> pdb=" O LEU E1489 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1489 through 1493' Processing helix chain 'E' and resid 1523 through 1528 removed outlier: 4.403A pdb=" N GLU E1527 " --> pdb=" O VAL E1524 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE E1528 " --> pdb=" O CYS E1525 " (cutoff:3.500A) Processing helix chain 'E' and resid 1610 through 1624 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) removed outlier: 3.504A pdb=" N SER E1624 " --> pdb=" O VAL E1620 " (cutoff:3.500A) Processing helix chain 'E' and resid 1629 through 1642 removed outlier: 3.804A pdb=" N ILE E1639 " --> pdb=" O GLY E1635 " (cutoff:3.500A) Processing helix chain 'E' and resid 1650 through 1662 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 1667 through 1672 Processing helix chain 'E' and resid 1683 through 1693 removed outlier: 3.530A pdb=" N ALA E1691 " --> pdb=" O GLU E1687 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 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 27 through 30 No H-bonds generated for 'chain 'G' and resid 27 through 30' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 86 through 98 Processing helix chain 'G' and resid 119 through 123 removed outlier: 3.850A pdb=" N LEU G 123 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 320 Processing helix chain 'I' and resid 360 through 363 No H-bonds generated for 'chain 'I' and resid 360 through 363' Processing helix chain 'I' and resid 385 through 394 Processing sheet with id= A, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id= B, 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= C, 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= D, 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= E, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.593A pdb=" N VAL C 24 " --> pdb=" O VAL C 38 " (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= F, 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= G, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.522A pdb=" N SER C 90 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 162 through 166 removed outlier: 4.768A pdb=" N ALA C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 147 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS C 133 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 173 through 178 removed outlier: 7.077A pdb=" N VAL C 188 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA C 176 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA C 186 " --> pdb=" O ALA C 176 " (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= J, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.682A pdb=" N LYS C 245 " --> pdb=" O THR C 237 " (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= K, first strand: chain 'C' and resid 306 through 308 removed outlier: 3.750A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 289 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 275 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 990 through 992 Processing sheet with id= M, first strand: chain 'I' and resid 329 through 333 Processing sheet with id= N, first strand: chain 'I' and resid 342 through 344 1248 hydrogen bonds defined for protein. 3549 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: 12.46 Time building geometry restraints manager: 11.93 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: 100.40 - 107.13: 854 107.13 - 113.86: 17195 113.86 - 120.59: 12341 120.59 - 127.32: 9746 127.32 - 134.05: 360 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: 6507 2.78 - 3.31: 28876 3.31 - 3.84: 44679 3.84 - 4.37: 54495 4.37 - 4.90: 92635 Nonbonded interactions: 227192 Sorted by model distance: nonbonded pdb=" OG SER C 55 " pdb=" OD1 ASN C 71 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR A 308 " pdb=" OG SER A1558 " model vdw 2.262 2.440 nonbonded pdb=" O LEU A1343 " pdb=" OG SER A1347 " model vdw 2.267 2.440 nonbonded pdb=" O LEU E 700 " pdb=" OG SER E 704 " model vdw 2.278 2.440 nonbonded pdb=" OG SER C 239 " pdb=" OD1 ASP C 241 " model vdw 2.280 2.440 ... (remaining 227187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 6.300 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: 24.010 Check model and map are aligned: 0.430 Set scattering table: 0.250 Process input model: 80.140 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.220 ------------------------------------------------------------------------------- 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 29829 Z= 0.134 Angle : 0.408 9.374 40496 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 : 4.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP E 750 HIS 0.002 0.000 HIS A2340 PHE 0.007 0.001 PHE A1122 TYR 0.009 0.001 TYR E 835 ARG 0.002 0.000 ARG A1538 *********************** 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 fitting. rotamer outliers: 49 poor density : 527 time to evaluate : 3.165 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: 0.4419 time to fit residues: 387.6103 Evaluate side-chains 369 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 352 time to evaluate : 3.201 ------------------------------------------------------------------------------- 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 320 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 297 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 345 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1398 HIS A1424 GLN ** A1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2055 HIS A2106 HIS C 28 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 ASN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29829 Z= 0.187 Angle : 0.514 9.838 40496 Z= 0.263 Chirality : 0.039 0.159 4700 Planarity : 0.004 0.053 5195 Dihedral : 4.312 59.912 4165 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.89 % Allowed : 8.57 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3768 helix: 0.86 (0.11), residues: 2275 sheet: -0.67 (0.38), residues: 183 loop : -0.99 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 27 HIS 0.008 0.001 HIS C 64 PHE 0.011 0.001 PHE A 316 TYR 0.014 0.001 TYR A2542 ARG 0.008 0.000 ARG G 94 *********************** 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 441 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 385 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8537 (mmtt) REVERT: A 1213 ILE cc_start: 0.8256 (tt) cc_final: 0.8045 (pt) REVERT: A 1377 ASP cc_start: 0.7287 (t70) cc_final: 0.6955 (t0) REVERT: A 1515 MET cc_start: 0.8871 (mtm) cc_final: 0.8281 (mtt) REVERT: A 1539 ASP cc_start: 0.7506 (t0) cc_final: 0.7242 (t0) REVERT: A 1925 GLU cc_start: 0.7779 (pt0) cc_final: 0.7565 (pt0) REVERT: A 1963 ASP cc_start: 0.6274 (m-30) cc_final: 0.5917 (m-30) REVERT: C 56 MET cc_start: 0.8172 (ttp) cc_final: 0.7944 (ttp) REVERT: C 95 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7522 (tm-30) REVERT: C 209 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6450 (pp30) REVERT: C 248 ARG cc_start: 0.7445 (ptm160) cc_final: 0.7154 (ptm160) REVERT: E 175 ASP cc_start: 0.7241 (t0) cc_final: 0.6806 (t0) REVERT: E 1524 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8472 (m) REVERT: G 6 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8885 (p0) REVERT: G 93 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8417 (tp) REVERT: I 404 MET cc_start: 0.2288 (tmm) cc_final: 0.1782 (ttt) outliers start: 56 outliers final: 35 residues processed: 426 average time/residue: 0.4023 time to fit residues: 272.9273 Evaluate side-chains 373 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 334 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1180 LEU 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 1644 VAL 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 2151 ILE Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain C residue 38 VAL 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 543 ASN 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 E residue 1679 ASP Chi-restraints excluded: chain G residue 6 ASN 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 383 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 287 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 345 optimal weight: 0.0060 chunk 373 optimal weight: 0.9990 chunk 307 optimal weight: 0.2980 chunk 342 optimal weight: 0.8980 chunk 117 optimal weight: 0.1980 chunk 277 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 827 GLN E1481 HIS G 34 HIS G 88 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29829 Z= 0.135 Angle : 0.460 11.249 40496 Z= 0.232 Chirality : 0.038 0.173 4700 Planarity : 0.003 0.051 5195 Dihedral : 4.193 57.438 4161 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.16 % Allowed : 9.82 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3768 helix: 1.10 (0.11), residues: 2270 sheet: -0.70 (0.38), residues: 180 loop : -1.02 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2429 HIS 0.008 0.001 HIS E1481 PHE 0.010 0.001 PHE A1122 TYR 0.011 0.001 TYR E 835 ARG 0.004 0.000 ARG A1028 *********************** 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 435 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 371 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8516 (mmtt) REVERT: A 1377 ASP cc_start: 0.7265 (t70) cc_final: 0.6929 (t0) REVERT: A 1481 MET cc_start: 0.8459 (mtt) cc_final: 0.8146 (mtt) REVERT: A 1539 ASP cc_start: 0.7470 (t0) cc_final: 0.7218 (t0) REVERT: A 1747 MET cc_start: 0.8538 (mmm) cc_final: 0.8284 (mmt) REVERT: A 1963 ASP cc_start: 0.6016 (m-30) cc_final: 0.5687 (m-30) REVERT: C 56 MET cc_start: 0.8144 (ttp) cc_final: 0.7923 (ttp) REVERT: C 95 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 209 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6424 (pp30) REVERT: E 908 ASN cc_start: 0.8510 (t0) cc_final: 0.8135 (t0) REVERT: E 1524 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8457 (m) REVERT: I 366 MET cc_start: 0.7004 (tpt) cc_final: 0.6699 (tpt) outliers start: 64 outliers final: 37 residues processed: 414 average time/residue: 0.4095 time to fit residues: 270.5106 Evaluate side-chains 373 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 334 time to evaluate : 3.335 ------------------------------------------------------------------------------- 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 936 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1590 MET 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 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 209 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 292 ASN 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 543 ASN 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 E residue 1679 ASP 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 341 optimal weight: 0.9980 chunk 259 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 164 optimal weight: 0.0070 chunk 232 optimal weight: 0.7980 chunk 346 optimal weight: 0.0370 chunk 367 optimal weight: 8.9990 chunk 181 optimal weight: 0.7980 chunk 328 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN E 540 HIS ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS G 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29829 Z= 0.146 Angle : 0.466 9.582 40496 Z= 0.233 Chirality : 0.038 0.178 4700 Planarity : 0.003 0.049 5195 Dihedral : 4.130 57.472 4159 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.02 % Allowed : 10.76 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3768 helix: 1.20 (0.11), residues: 2285 sheet: -0.68 (0.38), residues: 180 loop : -1.05 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2429 HIS 0.004 0.001 HIS A1084 PHE 0.011 0.001 PHE A1122 TYR 0.016 0.001 TYR C 184 ARG 0.006 0.000 ARG I 386 *********************** 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 411 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 351 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8519 (mmtt) REVERT: A 1377 ASP cc_start: 0.7265 (t70) cc_final: 0.6906 (t0) REVERT: A 1963 ASP cc_start: 0.6027 (m-30) cc_final: 0.5686 (m-30) REVERT: C 56 MET cc_start: 0.8143 (ttp) cc_final: 0.7916 (ttp) REVERT: C 95 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 209 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6456 (pp30) REVERT: E 908 ASN cc_start: 0.8529 (t0) cc_final: 0.8181 (t0) REVERT: E 1517 ASP cc_start: 0.7001 (t70) cc_final: 0.6637 (t70) REVERT: E 1524 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8437 (m) REVERT: I 401 MET cc_start: 0.7735 (ttm) cc_final: 0.7495 (ttm) outliers start: 60 outliers final: 42 residues processed: 395 average time/residue: 0.4087 time to fit residues: 260.4836 Evaluate side-chains 381 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 337 time to evaluate : 2.973 ------------------------------------------------------------------------------- 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 853 TYR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 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 1590 MET 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 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 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 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 421 VAL Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 587 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 898 VAL Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1649 ASP Chi-restraints excluded: chain E residue 1679 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 273 optimal weight: 0.0470 chunk 151 optimal weight: 0.7980 chunk 313 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 329 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN ** E 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1481 HIS G 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29829 Z= 0.169 Angle : 0.471 9.542 40496 Z= 0.237 Chirality : 0.039 0.160 4700 Planarity : 0.003 0.047 5195 Dihedral : 4.170 58.991 4159 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.36 % Allowed : 10.49 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3768 helix: 1.24 (0.11), residues: 2285 sheet: -0.83 (0.37), residues: 184 loop : -1.04 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2429 HIS 0.009 0.001 HIS E1481 PHE 0.013 0.001 PHE A1122 TYR 0.016 0.001 TYR E 835 ARG 0.006 0.000 ARG I 386 *********************** 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 421 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 351 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8512 (mmtt) REVERT: A 1377 ASP cc_start: 0.7260 (t70) cc_final: 0.6883 (t0) REVERT: A 1963 ASP cc_start: 0.6033 (m-30) cc_final: 0.5723 (m-30) REVERT: A 2052 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7736 (mt-10) REVERT: C 56 MET cc_start: 0.8150 (ttp) cc_final: 0.7928 (ttm) REVERT: C 95 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 209 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6460 (pm20) REVERT: E 533 ARG cc_start: 0.8296 (mpt180) cc_final: 0.7986 (mmt-90) REVERT: E 540 HIS cc_start: 0.6723 (m90) cc_final: 0.6491 (m170) REVERT: E 908 ASN cc_start: 0.8567 (t0) cc_final: 0.8223 (t0) REVERT: E 1517 ASP cc_start: 0.6962 (t70) cc_final: 0.6594 (t70) REVERT: E 1524 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8409 (m) REVERT: I 366 MET cc_start: 0.6707 (tpt) cc_final: 0.6362 (tpt) outliers start: 70 outliers final: 44 residues processed: 404 average time/residue: 0.4224 time to fit residues: 273.8311 Evaluate side-chains 379 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 333 time to evaluate : 2.804 ------------------------------------------------------------------------------- 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 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 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 1590 MET 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 1781 GLU 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 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 209 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 292 ASN 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 524 THR Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 637 SER 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 898 VAL Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1649 ASP Chi-restraints excluded: chain E residue 1679 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 4.9990 chunk 330 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 367 optimal weight: 6.9990 chunk 305 optimal weight: 0.0870 chunk 170 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29829 Z= 0.177 Angle : 0.481 9.808 40496 Z= 0.241 Chirality : 0.039 0.158 4700 Planarity : 0.003 0.047 5195 Dihedral : 4.165 59.829 4158 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.99 % Allowed : 11.30 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3768 helix: 1.26 (0.11), residues: 2285 sheet: -0.62 (0.38), residues: 183 loop : -1.13 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 546 HIS 0.007 0.001 HIS A1084 PHE 0.013 0.001 PHE A1122 TYR 0.015 0.001 TYR E 835 ARG 0.006 0.000 ARG G 94 *********************** 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 402 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 343 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1377 ASP cc_start: 0.7373 (t70) cc_final: 0.6977 (t0) REVERT: A 1963 ASP cc_start: 0.5980 (m-30) cc_final: 0.5661 (m-30) REVERT: A 2052 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7696 (mt-10) REVERT: C 56 MET cc_start: 0.8170 (ttp) cc_final: 0.7934 (ttm) REVERT: C 95 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 209 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: E 533 ARG cc_start: 0.8303 (mpt180) cc_final: 0.8001 (mmt-90) REVERT: E 908 ASN cc_start: 0.8579 (t0) cc_final: 0.8239 (t0) REVERT: E 1517 ASP cc_start: 0.7041 (t70) cc_final: 0.6713 (t70) REVERT: E 1524 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8388 (m) REVERT: I 404 MET cc_start: 0.2089 (tmm) cc_final: 0.1449 (ttt) outliers start: 59 outliers final: 46 residues processed: 387 average time/residue: 0.4185 time to fit residues: 258.6742 Evaluate side-chains 380 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 332 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 ILE 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 1023 VAL Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1313 MET Chi-restraints excluded: chain A residue 1427 GLU 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 A residue 1764 ILE Chi-restraints excluded: chain A residue 1781 GLU Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2151 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 A residue 2346 LEU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 292 ASN 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 524 THR Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 637 SER 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 898 VAL Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1649 ASP 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 383 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 209 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 208 optimal weight: 0.8980 chunk 309 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 366 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 HIS A2219 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS E 796 HIS E1481 HIS G 34 HIS G 88 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29829 Z= 0.172 Angle : 0.475 9.482 40496 Z= 0.239 Chirality : 0.039 0.158 4700 Planarity : 0.003 0.060 5195 Dihedral : 4.175 59.872 4158 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.99 % Allowed : 11.91 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3768 helix: 1.30 (0.11), residues: 2292 sheet: -0.61 (0.38), residues: 183 loop : -1.15 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2429 HIS 0.009 0.001 HIS E1481 PHE 0.013 0.001 PHE A1122 TYR 0.016 0.001 TYR C 184 ARG 0.006 0.000 ARG G 94 *********************** 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 396 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 337 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1377 ASP cc_start: 0.7361 (t70) cc_final: 0.6956 (t0) REVERT: A 1963 ASP cc_start: 0.5979 (m-30) cc_final: 0.5679 (m-30) REVERT: A 2052 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7705 (mt-10) REVERT: C 56 MET cc_start: 0.8099 (ttp) cc_final: 0.7889 (ttp) REVERT: C 95 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7575 (tm-30) REVERT: C 209 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: E 908 ASN cc_start: 0.8578 (t0) cc_final: 0.8244 (t0) REVERT: E 1517 ASP cc_start: 0.7037 (t70) cc_final: 0.6706 (t70) REVERT: E 1524 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8403 (m) REVERT: I 401 MET cc_start: 0.7812 (ttm) cc_final: 0.7442 (ttm) outliers start: 59 outliers final: 46 residues processed: 379 average time/residue: 0.4153 time to fit residues: 253.4162 Evaluate side-chains 374 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 326 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 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 1590 MET 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 1781 GLU 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 2173 THR Chi-restraints excluded: chain A residue 2181 GLU 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 A residue 2263 ILE Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 292 ASN 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 524 THR Chi-restraints excluded: chain E residue 587 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 898 VAL Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1649 ASP Chi-restraints excluded: chain E residue 1679 ASP 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 383 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 218 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 287 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 80 HIS E 209 ASN E 540 HIS E1481 HIS G 34 HIS G 88 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29829 Z= 0.206 Angle : 0.503 9.865 40496 Z= 0.251 Chirality : 0.040 0.182 4700 Planarity : 0.003 0.056 5195 Dihedral : 4.239 59.316 4158 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.13 % Allowed : 12.25 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3768 helix: 1.29 (0.11), residues: 2283 sheet: -0.61 (0.38), residues: 182 loop : -1.19 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 297 HIS 0.009 0.001 HIS E1481 PHE 0.014 0.001 PHE A1122 TYR 0.016 0.001 TYR E 835 ARG 0.009 0.000 ARG A1955 *********************** 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 391 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 328 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1377 ASP cc_start: 0.7366 (t70) cc_final: 0.6957 (t0) REVERT: A 1621 GLU cc_start: 0.7707 (mp0) cc_final: 0.7359 (mp0) REVERT: A 1963 ASP cc_start: 0.6009 (m-30) cc_final: 0.5739 (m-30) REVERT: C 95 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7610 (tm-30) REVERT: C 209 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.6581 (pm20) REVERT: E 1517 ASP cc_start: 0.7065 (t70) cc_final: 0.6759 (t70) REVERT: E 1524 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8403 (m) REVERT: I 401 MET cc_start: 0.7847 (ttm) cc_final: 0.7512 (ttm) REVERT: I 404 MET cc_start: 0.2335 (tmm) cc_final: 0.1385 (ttt) outliers start: 63 outliers final: 50 residues processed: 370 average time/residue: 0.4053 time to fit residues: 239.9538 Evaluate side-chains 376 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 324 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 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 1644 VAL Chi-restraints excluded: chain A residue 1648 GLU Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 1781 GLU Chi-restraints excluded: chain A residue 1931 GLN 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 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 2263 ILE Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 292 ASN 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 240 THR 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 540 HIS Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 637 SER 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 898 VAL Chi-restraints excluded: chain E residue 1481 HIS Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1649 ASP Chi-restraints excluded: chain E residue 1673 ILE 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 383 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 chunk 320 optimal weight: 0.0060 chunk 341 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 322 optimal weight: 1.9990 chunk 340 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1997 ASN A2219 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS G 88 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29829 Z= 0.188 Angle : 0.495 9.375 40496 Z= 0.247 Chirality : 0.039 0.228 4700 Planarity : 0.003 0.052 5195 Dihedral : 4.228 59.502 4158 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.02 % Allowed : 12.62 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3768 helix: 1.30 (0.11), residues: 2284 sheet: -0.62 (0.38), residues: 182 loop : -1.20 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2429 HIS 0.018 0.001 HIS E1481 PHE 0.013 0.001 PHE A1122 TYR 0.015 0.001 TYR C 184 ARG 0.008 0.000 ARG G 94 *********************** 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 387 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 327 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 MET cc_start: 0.5829 (tmm) cc_final: 0.5525 (ppp) REVERT: A 1377 ASP cc_start: 0.7319 (t70) cc_final: 0.6901 (t0) REVERT: A 1963 ASP cc_start: 0.6062 (m-30) cc_final: 0.5762 (m-30) REVERT: C 95 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7622 (tm-30) REVERT: C 209 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: E 908 ASN cc_start: 0.8588 (t0) cc_final: 0.8245 (t0) REVERT: E 1517 ASP cc_start: 0.7022 (t70) cc_final: 0.6717 (t70) REVERT: E 1524 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8398 (m) REVERT: I 353 GLN cc_start: 0.8189 (tp40) cc_final: 0.7775 (tm-30) REVERT: I 401 MET cc_start: 0.7807 (ttm) cc_final: 0.7494 (ttm) outliers start: 60 outliers final: 50 residues processed: 367 average time/residue: 0.4001 time to fit residues: 236.1428 Evaluate side-chains 369 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 317 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 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 1644 VAL Chi-restraints excluded: chain A residue 1648 GLU Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 1781 GLU Chi-restraints excluded: chain A residue 1931 GLN 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 2219 ASN Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2246 LEU Chi-restraints excluded: chain A residue 2263 ILE Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 292 ASN 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 240 THR 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 587 LEU Chi-restraints excluded: chain E residue 637 SER 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 898 VAL Chi-restraints excluded: chain E residue 1440 LYS Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1649 ASP Chi-restraints excluded: chain E residue 1673 ILE 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 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 220 optimal weight: 0.0570 chunk 171 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 378 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 chunk 301 optimal weight: 0.0050 chunk 31 optimal weight: 20.0000 chunk 232 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 overall best weight: 0.5914 ------------------------------------------------------------------------------- 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 80 HIS ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1481 HIS ** E1684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS G 88 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29829 Z= 0.170 Angle : 0.498 9.351 40496 Z= 0.248 Chirality : 0.039 0.248 4700 Planarity : 0.003 0.048 5195 Dihedral : 4.203 59.755 4158 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.99 % Allowed : 12.79 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3768 helix: 1.33 (0.11), residues: 2283 sheet: -0.62 (0.38), residues: 182 loop : -1.18 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A2429 HIS 0.013 0.001 HIS E1481 PHE 0.012 0.001 PHE A1122 TYR 0.015 0.001 TYR E 835 ARG 0.008 0.000 ARG G 94 ********************** 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 381 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 322 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 620 MET cc_start: 0.5780 (tmm) cc_final: 0.5469 (ppp) REVERT: A 1377 ASP cc_start: 0.7314 (t70) cc_final: 0.6890 (t0) REVERT: A 1963 ASP cc_start: 0.6038 (m-30) cc_final: 0.5726 (m-30) REVERT: C 95 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7620 (tm-30) REVERT: C 209 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: E 175 ASP cc_start: 0.7109 (t0) cc_final: 0.6844 (t0) REVERT: E 908 ASN cc_start: 0.8573 (t0) cc_final: 0.8237 (t0) REVERT: E 1517 ASP cc_start: 0.7043 (t70) cc_final: 0.6731 (t70) REVERT: E 1524 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8396 (m) REVERT: I 353 GLN cc_start: 0.8181 (tp40) cc_final: 0.7767 (tm-30) REVERT: I 401 MET cc_start: 0.7825 (ttm) cc_final: 0.7470 (ttm) outliers start: 59 outliers final: 47 residues processed: 361 average time/residue: 0.4193 time to fit residues: 246.2767 Evaluate side-chains 370 residues out of total 3383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 321 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1113 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 1648 GLU Chi-restraints excluded: chain A residue 1764 ILE Chi-restraints excluded: chain A residue 1781 GLU Chi-restraints excluded: chain A residue 1931 GLN 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 A residue 2263 ILE Chi-restraints excluded: chain A residue 2346 LEU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 292 ASN 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 524 THR Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain E residue 637 SER 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 898 VAL Chi-restraints excluded: chain E residue 1440 LYS Chi-restraints excluded: chain E residue 1524 VAL Chi-restraints excluded: chain E residue 1649 ASP Chi-restraints excluded: chain E residue 1673 ILE 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 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 6.9990 chunk 321 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 277 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 chunk 301 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 chunk 310 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1997 ASN C 28 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** E 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1684 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 = 0.3986 r_free = 0.3986 target = 0.142415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.109812 restraints weight = 52333.149| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.52 r_work: 0.3404 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29829 Z= 0.152 Angle : 0.487 9.424 40496 Z= 0.242 Chirality : 0.039 0.247 4700 Planarity : 0.003 0.047 5195 Dihedral : 4.135 59.717 4157 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.75 % Allowed : 13.26 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3768 helix: 1.36 (0.11), residues: 2288 sheet: -0.62 (0.38), residues: 182 loop : -1.18 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A2429 HIS 0.007 0.001 HIS E1481 PHE 0.012 0.001 PHE A1122 TYR 0.014 0.001 TYR E 835 ARG 0.008 0.000 ARG G 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6587.75 seconds wall clock time: 119 minutes 36.91 seconds (7176.91 seconds total)