Starting phenix.real_space_refine on Fri Mar 6 17:42:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pe9_13349/03_2026/7pe9_13349.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pe9_13349/03_2026/7pe9_13349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pe9_13349/03_2026/7pe9_13349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pe9_13349/03_2026/7pe9_13349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pe9_13349/03_2026/7pe9_13349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pe9_13349/03_2026/7pe9_13349.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1785 atoms to isotropic. 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 186 5.16 5 C 19661 2.51 5 N 5536 2.21 5 O 5686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31076 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2194, 16419 Classifications: {'peptide': 2194} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 88, 'TRANS': 2105} Chain breaks: 20 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1672 Unresolved non-hydrogen dihedrals: 1079 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'ASN:plan1': 10, 'GLN:plan1': 23, 'PHE:plan': 19, 'ARG:plan': 31, 'GLU:plan': 33, 'HIS:plan': 9, 'TYR:plan': 8, 'ASP:plan': 18, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 714 Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 8917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8917 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1077} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 2, 'GLU:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2580 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 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 24.339 72.610 159.100 1.00150.21 S ATOM 26981 SG CYS E1523 20.620 72.811 159.184 1.00152.50 S ATOM 27441 SG CYS E1651 22.439 75.846 157.870 1.00135.63 S Time building chain proxies: 6.34, per 1000 atoms: 0.20 Number of scatterers: 31076 At special positions: 0 Unit cell: (152.352, 155.526, 204.194, 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 186 16.00 P 6 15.00 O 5686 8.00 N 5536 7.00 C 19661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E4801 " pdb="ZN ZN E4801 " - pdb=" NE2 HIS E1515 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1523 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1520 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1651 " Number of angles added : 3 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7714 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 16 sheets defined 66.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 removed outlier: 3.634A pdb=" N VAL A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 74 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.510A pdb=" N ARG A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 135 removed outlier: 3.897A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 137 No H-bonds generated for 'chain 'A' and resid 136 through 137' Processing helix chain 'A' and resid 138 through 139 No H-bonds generated for 'chain 'A' and resid 138 through 139' Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.580A pdb=" N GLN A 185 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.953A pdb=" N GLU A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.891A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 376 Processing helix chain 'A' and resid 387 through 403 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.758A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 Processing helix chain 'A' and resid 451 through 463 removed outlier: 4.087A pdb=" N VAL A 455 " --> pdb=" O TYR A 451 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.505A pdb=" N PHE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 removed outlier: 4.399A pdb=" N GLU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 4.040A pdb=" N GLY A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.867A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 607 removed outlier: 3.548A pdb=" N HIS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.521A pdb=" N GLU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 666 removed outlier: 3.549A pdb=" N SER A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.659A pdb=" N ARG A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 686 removed outlier: 4.488A pdb=" N ALA A 685 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.780A pdb=" N ALA A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 699 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 720 removed outlier: 3.554A pdb=" N ARG A 708 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 717 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 4.003A pdb=" N VAL A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 764 Processing helix chain 'A' and resid 764 through 769 removed outlier: 3.708A pdb=" N ILE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 784 removed outlier: 3.818A pdb=" N ILE A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 809 removed outlier: 3.693A pdb=" N ASN A 797 " --> pdb=" O GLY A 793 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 removed outlier: 4.404A pdb=" N ILE A 822 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 Processing helix chain 'A' and resid 856 through 861 removed outlier: 4.021A pdb=" N LYS A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 861 " --> pdb=" O PRO A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 856 through 861' Processing helix chain 'A' and resid 863 through 875 removed outlier: 3.733A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 892 removed outlier: 3.605A pdb=" N ILE A 885 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 886 " --> pdb=" O ARG A 882 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 892 " --> pdb=" O LEU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.510A pdb=" N HIS A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 937 removed outlier: 3.719A pdb=" N VAL A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 958 removed outlier: 4.025A pdb=" N TYR A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Proline residue: A 948 - end of helix removed outlier: 3.525A pdb=" N VAL A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 960 No H-bonds generated for 'chain 'A' and resid 959 through 960' Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.610A pdb=" N LEU A 964 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS A 966 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 983 removed outlier: 3.824A pdb=" N VAL A 972 " --> pdb=" O HIS A 968 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 974 " --> pdb=" O MET A 970 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 977 " --> pdb=" O GLN A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 989 through 1004 Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1006 through 1023 removed outlier: 4.434A pdb=" N GLU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1041 removed outlier: 4.431A pdb=" N ASP A1032 " --> pdb=" O ARG A1028 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A1040 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A1041 " --> pdb=" O LEU A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1064 Processing helix chain 'A' and resid 1066 through 1073 removed outlier: 3.747A pdb=" N LEU A1071 " --> pdb=" O LYS A1068 " (cutoff:3.500A) Proline residue: A1072 - end of helix Processing helix chain 'A' and resid 1074 through 1080 removed outlier: 4.005A pdb=" N ARG A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1101 removed outlier: 4.048A pdb=" N ALA A1099 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1120 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1128 through 1144 removed outlier: 3.862A pdb=" N VAL A1139 " --> pdb=" O ALA A1135 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A1140 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1142 " --> pdb=" O THR A1138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1164 removed outlier: 3.932A pdb=" N HIS A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 4.160A pdb=" N ASP A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1182 removed outlier: 3.927A pdb=" N ASP A1175 " --> pdb=" O SER A1171 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1190 removed outlier: 3.859A pdb=" N TYR A1188 " --> pdb=" O GLY A1185 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1203 removed outlier: 3.749A pdb=" N LYS A1197 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A1198 " --> pdb=" O MET A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1218 removed outlier: 3.505A pdb=" N VAL A1211 " --> pdb=" O GLN A1207 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1212 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1238 Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 4.029A pdb=" N ALA A1268 " --> pdb=" O ASN A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1294 removed outlier: 3.630A pdb=" N ASP A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1302 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 3.686A pdb=" N ALA A1309 " --> pdb=" O ALA A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 removed outlier: 3.603A pdb=" N ARG A1315 " --> pdb=" O ASN A1311 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1311 through 1316' Processing helix chain 'A' and resid 1317 through 1329 removed outlier: 3.521A pdb=" N SER A1324 " --> pdb=" O ALA A1320 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1346 removed outlier: 3.619A pdb=" N GLU A1336 " --> pdb=" O ASP A1332 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A1337 " --> pdb=" O GLN A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1367 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1379 through 1389 removed outlier: 3.683A pdb=" N ALA A1388 " --> pdb=" O GLY A1384 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A1389 " --> pdb=" O GLU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1407 removed outlier: 3.724A pdb=" N LYS A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A1407 " --> pdb=" O GLU A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1422 Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.550A pdb=" N VAL A1432 " --> pdb=" O ALA A1428 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1433 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 4.253A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A1451 " --> pdb=" O ALA A1447 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1453 " --> pdb=" O TRP A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1469 removed outlier: 3.540A pdb=" N VAL A1461 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A1469 " --> pdb=" O LYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 removed outlier: 3.531A pdb=" N MET A1481 " --> pdb=" O MET A1477 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1486 " --> pdb=" O ARG A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1501 removed outlier: 3.763A pdb=" N GLN A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1524 removed outlier: 3.685A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1534 removed outlier: 3.929A pdb=" N GLU A1530 " --> pdb=" O TRP A1526 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS A1534 " --> pdb=" O GLU A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 removed outlier: 3.502A pdb=" N ALA A1544 " --> pdb=" O THR A1540 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1550 " --> pdb=" O TYR A1546 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A1553 " --> pdb=" O VAL A1549 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A1554 " --> pdb=" O LEU A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1580 removed outlier: 3.525A pdb=" N ALA A1560 " --> pdb=" O LEU A1556 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A1562 " --> pdb=" O SER A1558 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A1569 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1570 " --> pdb=" O LYS A1566 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A1577 " --> pdb=" O ALA A1573 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET A1578 " --> pdb=" O GLU A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1588 removed outlier: 3.535A pdb=" N TYR A1587 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A1588 " --> pdb=" O ARG A1585 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1584 through 1588' Processing helix chain 'A' and resid 1589 through 1608 removed outlier: 3.838A pdb=" N GLU A1600 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1601 " --> pdb=" O SER A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1609 through 1612 removed outlier: 3.780A pdb=" N ARG A1612 " --> pdb=" O PRO A1609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1609 through 1612' Processing helix chain 'A' and resid 1614 through 1622 removed outlier: 5.427A pdb=" N TRP A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A1621 " --> pdb=" O GLN A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1640 removed outlier: 3.520A pdb=" N MET A1638 " --> pdb=" O GLN A1634 " (cutoff:3.500A) Processing helix chain 'A' and resid 1645 through 1648 Processing helix chain 'A' and resid 1649 through 1664 removed outlier: 3.851A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS A1655 " --> pdb=" O ARG A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 removed outlier: 3.854A pdb=" N LEU A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A1676 " --> pdb=" O THR A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1707 Processing helix chain 'A' and resid 1709 through 1729 removed outlier: 3.540A pdb=" N GLN A1715 " --> pdb=" O ILE A1711 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN A1725 " --> pdb=" O VAL A1721 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A1726 " --> pdb=" O GLN A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1763 removed outlier: 3.574A pdb=" N ALA A1748 " --> pdb=" O HIS A1744 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1783 removed outlier: 3.731A pdb=" N LYS A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A1781 " --> pdb=" O SER A1777 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1809 removed outlier: 3.721A pdb=" N ALA A1792 " --> pdb=" O LYS A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1877 through 1896 removed outlier: 3.565A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix removed outlier: 3.538A pdb=" N ARG A1896 " --> pdb=" O ILE A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1914 removed outlier: 4.109A pdb=" N LEU A1907 " --> pdb=" O THR A1903 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A1908 " --> pdb=" O LEU A1904 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1909 " --> pdb=" O ARG A1905 " (cutoff:3.500A) Processing helix chain 'A' and resid 1916 through 1930 removed outlier: 3.769A pdb=" N ASN A1920 " --> pdb=" O TRP A1916 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A1921 " --> pdb=" O PRO A1917 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A1922 " --> pdb=" O ASP A1918 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A1925 " --> pdb=" O GLU A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1945 removed outlier: 3.976A pdb=" N ARG A1945 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1968 removed outlier: 4.677A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A1957 " --> pdb=" O VAL A1953 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A1958 " --> pdb=" O GLY A1954 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A1960 " --> pdb=" O LEU A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1981 Processing helix chain 'A' and resid 1984 through 1999 removed outlier: 3.544A pdb=" N ILE A1994 " --> pdb=" O ALA A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2021 removed outlier: 4.398A pdb=" N VAL A2006 " --> pdb=" O SER A2002 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A2007 " --> pdb=" O ASN A2003 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A2021 " --> pdb=" O ILE A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2041 Processing helix chain 'A' and resid 2044 through 2057 removed outlier: 3.796A pdb=" N GLU A2049 " --> pdb=" O LYS A2045 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A2050 " --> pdb=" O GLY A2046 " (cutoff:3.500A) Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2074 Processing helix chain 'A' and resid 2074 through 2092 removed outlier: 3.568A pdb=" N GLU A2083 " --> pdb=" O MET A2079 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A2090 " --> pdb=" O ARG A2086 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2113 removed outlier: 3.784A pdb=" N LEU A2097 " --> pdb=" O ASN A2093 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A2103 " --> pdb=" O GLN A2099 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2192 through 2211 removed outlier: 3.708A pdb=" N ARG A2197 " --> pdb=" O ARG A2193 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2217 removed outlier: 3.528A pdb=" N ARG A2217 " --> pdb=" O PRO A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2257 removed outlier: 3.584A pdb=" N TYR A2253 " --> pdb=" O LEU A2249 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2279 through 2294 removed outlier: 3.604A pdb=" N GLU A2285 " --> pdb=" O MET A2281 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A2292 " --> pdb=" O GLU A2288 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2306 removed outlier: 3.851A pdb=" N TRP A2304 " --> pdb=" O ALA A2300 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A2306 " --> pdb=" O LEU A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2335 removed outlier: 3.919A pdb=" N VAL A2326 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A2327 " --> pdb=" O SER A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2340 through 2342 No H-bonds generated for 'chain 'A' and resid 2340 through 2342' Processing helix chain 'A' and resid 2363 through 2368 removed outlier: 3.705A pdb=" N THR A2367 " --> pdb=" O GLU A2363 " (cutoff:3.500A) Processing helix chain 'A' and resid 2380 through 2385 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2410 through 2423 removed outlier: 3.746A pdb=" N VAL A2417 " --> pdb=" O SER A2413 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2428 through 2432 Processing helix chain 'A' and resid 2494 through 2508 removed outlier: 3.657A pdb=" N GLN A2499 " --> pdb=" O LYS A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2533 Processing helix chain 'A' and resid 2534 through 2540 removed outlier: 3.857A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'E' and resid 32 through 43 removed outlier: 4.016A pdb=" N ARG E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 52 through 70 Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.536A pdb=" N ILE E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.796A pdb=" N LEU E 123 " --> pdb=" O LYS E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.656A pdb=" N ARG E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP E 134 " --> pdb=" O ALA E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 157 removed outlier: 3.652A pdb=" N GLN E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 161 removed outlier: 3.838A pdb=" N PHE E 161 " --> pdb=" O ALA E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 161' Processing helix chain 'E' and resid 162 through 175 removed outlier: 3.604A pdb=" N THR E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 removed outlier: 3.502A pdb=" N ILE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.854A pdb=" N VAL E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 removed outlier: 3.701A pdb=" N THR E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 235 removed outlier: 3.515A pdb=" N ILE E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.564A pdb=" N ILE E 253 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 272 through 293 removed outlier: 3.517A pdb=" N GLU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 302 removed outlier: 3.660A pdb=" N ILE E 299 " --> pdb=" O TRP E 295 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 315 removed outlier: 3.598A pdb=" N SER E 311 " --> pdb=" O SER E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 321 through 335 removed outlier: 3.682A pdb=" N ARG E 325 " --> pdb=" O MET E 321 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 352 removed outlier: 3.594A pdb=" N ALA E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 363 removed outlier: 3.650A pdb=" N TRP E 362 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG E 363 " --> pdb=" O ASP E 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 359 through 363' Processing helix chain 'E' and resid 369 through 375 removed outlier: 4.138A pdb=" N THR E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 403 removed outlier: 3.638A pdb=" N ASN E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 414 Processing helix chain 'E' and resid 416 through 435 removed outlier: 3.895A pdb=" N VAL E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 426 " --> pdb=" O ARG E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 444 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 462 through 486 removed outlier: 3.573A pdb=" N LEU E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 478 " --> pdb=" O ASN E 474 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE E 479 " --> pdb=" O CYS E 475 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU E 481 " --> pdb=" O LYS E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 505 removed outlier: 3.581A pdb=" N ILE E 497 " --> pdb=" O HIS E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.671A pdb=" N LEU E 528 " --> pdb=" O THR E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 556 removed outlier: 3.531A pdb=" N ILE E 551 " --> pdb=" O ASN E 547 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY E 552 " --> pdb=" O TRP E 548 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 553 " --> pdb=" O ASN E 549 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 582 removed outlier: 3.803A pdb=" N PHE E 580 " --> pdb=" O ARG E 576 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 615 removed outlier: 3.514A pdb=" N LEU E 601 " --> pdb=" O LYS E 597 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE E 611 " --> pdb=" O GLN E 607 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 615 " --> pdb=" O PHE E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 638 removed outlier: 3.993A pdb=" N GLN E 620 " --> pdb=" O GLU E 616 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLY E 621 " --> pdb=" O GLU E 617 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR E 622 " --> pdb=" O ASP E 618 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP E 625 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 626 " --> pdb=" O TYR E 622 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER E 638 " --> pdb=" O LEU E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 652 removed outlier: 4.170A pdb=" N GLY E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU E 652 " --> pdb=" O ASN E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 658 removed outlier: 3.787A pdb=" N GLN E 657 " --> pdb=" O THR E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 665 Processing helix chain 'E' and resid 669 through 680 removed outlier: 3.653A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET E 675 " --> pdb=" O HIS E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 688 Processing helix chain 'E' and resid 695 through 705 removed outlier: 3.568A pdb=" N SER E 703 " --> pdb=" O LYS E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 711 through 723 removed outlier: 3.781A pdb=" N VAL E 715 " --> pdb=" O GLY E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 735 removed outlier: 3.608A pdb=" N TYR E 731 " --> pdb=" O ALA E 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 751 removed outlier: 3.990A pdb=" N TRP E 750 " --> pdb=" O PHE E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 758 removed outlier: 3.760A pdb=" N THR E 757 " --> pdb=" O GLU E 753 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN E 758 " --> pdb=" O LEU E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 761 No H-bonds generated for 'chain 'E' and resid 759 through 761' Processing helix chain 'E' and resid 763 through 778 removed outlier: 3.514A pdb=" N ASP E 772 " --> pdb=" O SER E 768 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 777 " --> pdb=" O ILE E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 780 through 789 Processing helix chain 'E' and resid 798 through 806 Processing helix chain 'E' and resid 807 through 810 Processing helix chain 'E' and resid 811 through 819 removed outlier: 3.553A pdb=" N TYR E 817 " --> pdb=" O LYS E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 831 removed outlier: 3.588A pdb=" N GLU E 829 " --> pdb=" O ALA E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 851 removed outlier: 3.705A pdb=" N ASP E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 881 through 886 Processing helix chain 'E' and resid 889 through 899 removed outlier: 3.671A pdb=" N LEU E 895 " --> pdb=" O THR E 891 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 896 " --> pdb=" O GLY E 892 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 897 " --> pdb=" O CYS E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 911 removed outlier: 3.509A pdb=" N ASN E 908 " --> pdb=" O GLU E 904 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 909 " --> pdb=" O LEU E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 934 removed outlier: 3.976A pdb=" N LYS E 921 " --> pdb=" O TRP E 917 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 923 " --> pdb=" O GLU E 919 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA E 929 " --> pdb=" O ALA E 925 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN E 932 " --> pdb=" O TRP E 928 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE E 933 " --> pdb=" O ALA E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 936 through 941 Processing helix chain 'E' and resid 948 through 956 Processing helix chain 'E' and resid 961 through 976 removed outlier: 3.987A pdb=" N VAL E 969 " --> pdb=" O ARG E 965 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR E 970 " --> pdb=" O GLY E 966 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 973 " --> pdb=" O VAL E 969 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 974 " --> pdb=" O TYR E 970 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 975 " --> pdb=" O VAL E 971 " (cutoff:3.500A) Processing helix chain 'E' and resid 978 through 988 removed outlier: 3.669A pdb=" N ILE E 984 " --> pdb=" O GLN E 980 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS E 988 " --> pdb=" O ILE E 984 " (cutoff:3.500A) Processing helix chain 'E' and resid 1432 through 1436 removed outlier: 3.690A pdb=" N ILE E1436 " --> pdb=" O ILE E1433 " (cutoff:3.500A) Processing helix chain 'E' and resid 1480 through 1485 removed outlier: 4.241A pdb=" N GLN E1485 " --> pdb=" O HIS E1481 " (cutoff:3.500A) Processing helix chain 'E' and resid 1488 through 1494 removed outlier: 3.739A pdb=" N MET E1493 " --> pdb=" O LEU E1489 " (cutoff:3.500A) Processing helix chain 'E' and resid 1522 through 1526 removed outlier: 3.515A pdb=" N ILE E1526 " --> pdb=" O CYS E1523 " (cutoff:3.500A) Processing helix chain 'E' and resid 1609 through 1623 removed outlier: 3.732A pdb=" N ARG E1613 " --> pdb=" O ARG E1609 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS E1614 " --> pdb=" O ILE E1610 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU E1615 " --> pdb=" O LEU E1611 " (cutoff:3.500A) Processing helix chain 'E' and resid 1628 through 1643 removed outlier: 3.626A pdb=" N HIS E1632 " --> pdb=" O SER E1628 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE E1639 " --> pdb=" O GLY E1635 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E1640 " --> pdb=" O LEU E1636 " (cutoff:3.500A) Processing helix chain 'E' and resid 1649 through 1663 removed outlier: 3.716A pdb=" N HIS E1662 " --> pdb=" O HIS E1658 " (cutoff:3.500A) Processing helix chain 'E' and resid 1666 through 1673 Processing helix chain 'E' and resid 1682 through 1694 removed outlier: 3.862A pdb=" N HIS E1686 " --> pdb=" O PHE E1682 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 21 removed outlier: 3.622A pdb=" N ALA G 12 " --> pdb=" O THR G 8 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 85 through 100 removed outlier: 3.959A pdb=" N GLU G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN G 98 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 removed outlier: 4.051A pdb=" N PHE G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 48 removed outlier: 3.812A pdb=" N ARG I 29 " --> pdb=" O ARG I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 77 removed outlier: 3.647A pdb=" N ILE I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP I 71 " --> pdb=" O LYS I 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP I 72 " --> pdb=" O GLU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 96 Processing helix chain 'I' and resid 119 through 121 No H-bonds generated for 'chain 'I' and resid 119 through 121' Processing helix chain 'I' and resid 127 through 145 Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 182 through 197 removed outlier: 3.584A pdb=" N ARG I 192 " --> pdb=" O GLN I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 315 through 321 Processing helix chain 'I' and resid 359 through 364 Processing helix chain 'I' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 removed outlier: 3.952A pdb=" N GLN A2161 " --> pdb=" O LYS A2171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.921A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2184 through 2188 Processing sheet with id=AA4, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 39 removed outlier: 3.545A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 321 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS C 317 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 50 removed outlier: 4.116A pdb=" N ALA C 47 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 60 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.671A pdb=" N GLY C 103 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL C 91 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR C 101 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE C 93 " --> pdb=" O TRP C 99 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TRP C 99 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 136 removed outlier: 6.979A pdb=" N GLY C 146 " --> pdb=" O ASN C 132 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 134 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 144 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU C 136 " --> pdb=" O GLU C 142 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU C 142 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 173 through 178 removed outlier: 7.117A pdb=" N VAL C 188 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA C 176 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA C 186 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS C 194 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS C 215 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C 196 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 211 " --> pdb=" O ASN C 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 223 through 228 removed outlier: 4.286A pdb=" N GLN C 225 " --> pdb=" O CYS C 238 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 245 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 239 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.537A pdb=" N SER C 289 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 306 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 990 through 992 Processing sheet with id=AB4, first strand: chain 'I' and resid 51 through 55 removed outlier: 5.245A pdb=" N LYS I 51 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN I 62 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N ASN I 62 " --> pdb=" O PHE I 117 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE I 117 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 152 through 156 removed outlier: 6.224A pdb=" N ARG I 154 " --> pdb=" O GLU I 162 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLU I 162 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU I 156 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS I 160 " --> pdb=" O GLU I 156 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ARG I 163 " --> pdb=" O PHE I 217 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE I 217 " --> pdb=" O ARG I 163 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE I 165 " --> pdb=" O TYR I 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 329 through 333 removed outlier: 4.871A pdb=" N SER I 374 " --> pdb=" O GLU I 402 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 342 through 344 removed outlier: 6.774A pdb=" N VAL I 343 " --> pdb=" O GLN I 353 " (cutoff:3.500A) 1592 hydrogen bonds defined for protein. 4659 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: 7.41 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10446 1.34 - 1.46: 6734 1.46 - 1.58: 14171 1.58 - 1.70: 6 1.70 - 1.82: 292 Bond restraints: 31649 Sorted by residual: bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.588 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.596 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O15 IHP A2601 " pdb=" P5 IHP A2601 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O16 IHP A2601 " pdb=" P6 IHP A2601 " ideal model delta sigma weight residual 1.672 1.611 0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" C5 IHP A2601 " pdb=" O15 IHP A2601 " ideal model delta sigma weight residual 1.389 1.443 -0.054 2.00e-02 2.50e+03 7.18e+00 ... (remaining 31644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 42351 1.86 - 3.72: 482 3.72 - 5.58: 80 5.58 - 7.44: 13 7.44 - 9.30: 5 Bond angle restraints: 42931 Sorted by residual: angle pdb=" CG ARG I 218 " pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " ideal model delta sigma weight residual 112.00 121.28 -9.28 2.20e+00 2.07e-01 1.78e+01 angle pdb=" C GLN C 41 " pdb=" N ASP C 42 " pdb=" CA ASP C 42 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " pdb=" CZ ARG I 218 " ideal model delta sigma weight residual 124.40 128.12 -3.72 1.40e+00 5.10e-01 7.07e+00 angle pdb=" CA LEU A 811 " pdb=" CB LEU A 811 " pdb=" CG LEU A 811 " ideal model delta sigma weight residual 116.30 125.51 -9.21 3.50e+00 8.16e-02 6.93e+00 angle pdb=" C GLU E 834 " pdb=" N TYR E 835 " pdb=" CA TYR E 835 " ideal model delta sigma weight residual 122.79 118.56 4.23 1.63e+00 3.76e-01 6.72e+00 ... (remaining 42926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17295 17.92 - 35.85: 1513 35.85 - 53.77: 288 53.77 - 71.69: 46 71.69 - 89.62: 27 Dihedral angle restraints: 19169 sinusoidal: 7345 harmonic: 11824 Sorted by residual: dihedral pdb=" CG ARG I 218 " pdb=" CD ARG I 218 " pdb=" NE ARG I 218 " pdb=" CZ ARG I 218 " ideal model delta sinusoidal sigma weight residual -90.00 -23.20 -66.80 2 1.50e+01 4.44e-03 1.80e+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 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+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 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 19166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4286 0.058 - 0.116: 631 0.116 - 0.174: 30 0.174 - 0.233: 3 0.233 - 0.291: 3 Chirality restraints: 4953 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 2.61 -0.29 2.00e-01 2.50e+01 2.11e+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 1.65e+00 chirality pdb=" CB ILE A1048 " pdb=" CA ILE A1048 " pdb=" CG1 ILE A1048 " pdb=" CG2 ILE A1048 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4950 not shown) Planarity restraints: 5513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 51 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO C 52 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 52 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 52 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1689 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A1690 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1690 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1690 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1075 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO A1076 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1076 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1076 " -0.028 5.00e-02 4.00e+02 ... (remaining 5510 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6785 2.78 - 3.31: 30328 3.31 - 3.84: 47605 3.84 - 4.37: 57237 4.37 - 4.90: 97513 Nonbonded interactions: 239468 Sorted by model distance: nonbonded pdb=" OD2 ASP C 106 " pdb=" OG1 THR C 108 " model vdw 2.250 3.040 nonbonded pdb=" O GLN I 152 " pdb=" OG1 THR I 164 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR E1522 " pdb=" O GLN E1532 " model vdw 2.264 3.040 nonbonded pdb=" NE2 GLN C 122 " pdb=" O ARG G 111 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR C 51 " pdb=" O MET C 56 " model vdw 2.299 3.040 ... (remaining 239463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 32.800 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.003 0.115 31654 Z= 0.158 Angle : 0.550 9.303 42934 Z= 0.282 Chirality : 0.041 0.291 4953 Planarity : 0.003 0.053 5513 Dihedral : 14.276 89.616 11455 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.33 % Allowed : 1.77 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3977 helix: 0.07 (0.11), residues: 2373 sheet: -0.56 (0.36), residues: 196 loop : -1.08 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1514 TYR 0.027 0.001 TYR E 835 PHE 0.017 0.001 PHE I 217 TRP 0.025 0.001 TRP C 27 HIS 0.006 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00319 (31649) covalent geometry : angle 0.54872 (42931) hydrogen bonds : bond 0.28885 ( 1592) hydrogen bonds : angle 7.05901 ( 4659) metal coordination : bond 0.00735 ( 4) metal coordination : angle 4.11847 ( 3) Misc. bond : bond 0.11472 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 769 time to evaluate : 1.224 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: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9431 (t) cc_final: 0.9155 (t) REVERT: A 630 LEU cc_start: 0.9116 (mt) cc_final: 0.8896 (tp) REVERT: A 700 LEU cc_start: 0.7325 (mp) cc_final: 0.6968 (mp) REVERT: A 701 ASN cc_start: 0.7751 (m-40) cc_final: 0.7505 (p0) REVERT: A 756 MET cc_start: 0.9078 (mtp) cc_final: 0.8747 (mmm) REVERT: A 768 ILE cc_start: 0.8018 (mm) cc_final: 0.7739 (tp) REVERT: A 772 MET cc_start: 0.8867 (mmp) cc_final: 0.8127 (mmt) REVERT: A 813 MET cc_start: 0.8302 (ttm) cc_final: 0.8086 (ttp) REVERT: A 1031 MET cc_start: 0.9153 (tpt) cc_final: 0.8920 (tpp) REVERT: A 1083 MET cc_start: 0.7527 (ppp) cc_final: 0.7286 (ppp) REVERT: A 1108 ASP cc_start: 0.8085 (m-30) cc_final: 0.7668 (p0) REVERT: A 1153 SER cc_start: 0.9080 (p) cc_final: 0.8763 (t) REVERT: A 1154 ARG cc_start: 0.8556 (tpp80) cc_final: 0.8000 (ttt180) REVERT: A 1228 ASP cc_start: 0.8384 (t70) cc_final: 0.8095 (t0) REVERT: A 1287 LEU cc_start: 0.8866 (tp) cc_final: 0.8165 (tp) REVERT: A 1311 ASN cc_start: 0.8663 (m-40) cc_final: 0.8460 (m-40) REVERT: A 1355 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8619 (tp40) REVERT: A 1359 ASN cc_start: 0.8731 (m-40) cc_final: 0.8487 (m110) REVERT: A 1477 MET cc_start: 0.8993 (ppp) cc_final: 0.8488 (ppp) REVERT: A 1527 ASP cc_start: 0.8287 (t0) cc_final: 0.8066 (t0) REVERT: A 1530 GLU cc_start: 0.8271 (tp30) cc_final: 0.7642 (tm-30) REVERT: A 1542 ASP cc_start: 0.8528 (m-30) cc_final: 0.8256 (t0) REVERT: A 1559 LEU cc_start: 0.8791 (tp) cc_final: 0.8419 (tp) REVERT: A 1632 ASP cc_start: 0.8380 (m-30) cc_final: 0.8164 (m-30) REVERT: A 1650 MET cc_start: 0.8141 (mpp) cc_final: 0.7843 (mpp) REVERT: A 1665 ARG cc_start: 0.8279 (mpp-170) cc_final: 0.7743 (ptp90) REVERT: A 1967 TYR cc_start: 0.9068 (m-80) cc_final: 0.8776 (m-10) REVERT: A 2003 ASN cc_start: 0.8800 (t0) cc_final: 0.8470 (t0) REVERT: A 2058 MET cc_start: 0.8824 (mtt) cc_final: 0.8618 (mtt) REVERT: A 2298 ASP cc_start: 0.8940 (m-30) cc_final: 0.8066 (m-30) REVERT: A 2324 LEU cc_start: 0.9560 (tp) cc_final: 0.9358 (tp) REVERT: A 2424 ASP cc_start: 0.8928 (t0) cc_final: 0.8625 (t0) REVERT: A 2521 VAL cc_start: 0.9629 (t) cc_final: 0.8573 (t) REVERT: C 118 ASN cc_start: 0.8895 (t0) cc_final: 0.8119 (t0) REVERT: C 135 CYS cc_start: 0.7900 (t) cc_final: 0.7492 (t) REVERT: C 147 ASP cc_start: 0.8587 (p0) cc_final: 0.8093 (p0) REVERT: C 166 ILE cc_start: 0.7865 (tt) cc_final: 0.7349 (mp) REVERT: C 185 MET cc_start: 0.7223 (tmm) cc_final: 0.6557 (tmm) REVERT: C 195 TYR cc_start: 0.7237 (m-10) cc_final: 0.6797 (m-10) REVERT: C 247 TRP cc_start: 0.8488 (m100) cc_final: 0.8130 (m100) REVERT: C 255 MET cc_start: 0.8104 (tpt) cc_final: 0.7791 (mmt) REVERT: C 273 MET cc_start: 0.8138 (ttt) cc_final: 0.7843 (ttm) REVERT: C 307 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7064 (tm-30) REVERT: E 54 MET cc_start: 0.8939 (mmp) cc_final: 0.8733 (mmp) REVERT: E 81 TYR cc_start: 0.8261 (m-80) cc_final: 0.7789 (m-80) REVERT: E 124 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8106 (mmmm) REVERT: E 247 ASP cc_start: 0.8048 (m-30) cc_final: 0.7797 (t0) REVERT: E 249 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7893 (mm-30) REVERT: E 251 GLU cc_start: 0.8768 (mp0) cc_final: 0.8348 (mt-10) REVERT: E 372 GLU cc_start: 0.8357 (tt0) cc_final: 0.8046 (pt0) REVERT: E 475 CYS cc_start: 0.8387 (m) cc_final: 0.8012 (m) REVERT: E 523 ASP cc_start: 0.5638 (m-30) cc_final: 0.5412 (m-30) REVERT: E 545 GLU cc_start: 0.6209 (tp30) cc_final: 0.5787 (tp30) REVERT: E 564 ASN cc_start: 0.8058 (m110) cc_final: 0.7735 (t0) REVERT: E 565 TYR cc_start: 0.4667 (m-80) cc_final: 0.3983 (m-10) REVERT: E 577 LEU cc_start: 0.9259 (tp) cc_final: 0.8934 (tt) REVERT: E 684 CYS cc_start: 0.8833 (t) cc_final: 0.8574 (t) REVERT: E 696 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7222 (p90) REVERT: E 737 ARG cc_start: 0.8391 (ttm170) cc_final: 0.7984 (ptp-110) REVERT: E 775 ASP cc_start: 0.8744 (t70) cc_final: 0.8543 (t0) REVERT: E 779 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7438 (tm-30) REVERT: E 1424 TYR cc_start: 0.8818 (m-10) cc_final: 0.8596 (m-10) REVERT: E 1514 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8005 (tm-30) REVERT: E 1642 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8229 (tptt) REVERT: G 26 MET cc_start: 0.7837 (mmt) cc_final: 0.6967 (mmm) REVERT: G 27 CYS cc_start: 0.9197 (m) cc_final: 0.8551 (m) REVERT: I 23 GLN cc_start: 0.3418 (OUTLIER) cc_final: 0.3156 (pp30) REVERT: I 134 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.9029 (ptt) REVERT: I 149 THR cc_start: 0.3566 (OUTLIER) cc_final: 0.3134 (p) REVERT: I 164 THR cc_start: 0.1175 (OUTLIER) cc_final: 0.0519 (p) REVERT: I 171 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6946 (mt) REVERT: I 212 ASN cc_start: 0.9043 (p0) cc_final: 0.8657 (t0) REVERT: I 219 MET cc_start: 0.8681 (tpp) cc_final: 0.8289 (tmm) REVERT: I 319 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8662 (tt) REVERT: I 326 TYR cc_start: 0.6928 (p90) cc_final: 0.6452 (p90) REVERT: I 376 ASN cc_start: 0.8853 (p0) cc_final: 0.8319 (m-40) REVERT: I 403 VAL cc_start: 0.7675 (m) cc_final: 0.7165 (m) outliers start: 42 outliers final: 10 residues processed: 800 average time/residue: 0.2127 time to fit residues: 263.8788 Evaluate side-chains 437 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 420 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 383 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0070 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 GLN A 759 HIS ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1604 GLN A1719 HIS ** A1758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1806 HIS A1959 GLN C 64 HIS E 49 GLN E 59 HIS ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN I 56 HIS ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN I 390 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.096150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071411 restraints weight = 96823.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074282 restraints weight = 57940.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074417 restraints weight = 31616.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.075131 restraints weight = 25672.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075232 restraints weight = 21784.566| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31654 Z= 0.146 Angle : 0.653 13.635 42934 Z= 0.334 Chirality : 0.042 0.339 4953 Planarity : 0.005 0.051 5513 Dihedral : 5.151 77.442 4408 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.53 % Allowed : 10.33 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3977 helix: 0.50 (0.11), residues: 2435 sheet: -0.35 (0.37), residues: 197 loop : -1.15 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 192 TYR 0.028 0.001 TYR A2542 PHE 0.020 0.001 PHE E 611 TRP 0.023 0.001 TRP A1269 HIS 0.008 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00309 (31649) covalent geometry : angle 0.65323 (42931) hydrogen bonds : bond 0.05669 ( 1592) hydrogen bonds : angle 4.69722 ( 4659) metal coordination : bond 0.00962 ( 4) metal coordination : angle 1.47347 ( 3) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 479 time to evaluate : 1.168 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9273 (t) cc_final: 0.8925 (t) REVERT: A 620 MET cc_start: 0.8205 (tpp) cc_final: 0.7968 (mmt) REVERT: A 629 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7630 (mm) REVERT: A 630 LEU cc_start: 0.9150 (mt) cc_final: 0.8896 (tp) REVERT: A 679 LEU cc_start: 0.9548 (mm) cc_final: 0.9149 (mm) REVERT: A 700 LEU cc_start: 0.8471 (mp) cc_final: 0.8061 (mp) REVERT: A 701 ASN cc_start: 0.8378 (m-40) cc_final: 0.8089 (p0) REVERT: A 768 ILE cc_start: 0.8953 (mm) cc_final: 0.8677 (tp) REVERT: A 816 TRP cc_start: 0.7933 (m100) cc_final: 0.7418 (m100) REVERT: A 1115 LEU cc_start: 0.8766 (tt) cc_final: 0.8466 (tp) REVERT: A 1228 ASP cc_start: 0.8073 (t70) cc_final: 0.7194 (t0) REVERT: A 1359 ASN cc_start: 0.8745 (m-40) cc_final: 0.8216 (m110) REVERT: A 1477 MET cc_start: 0.8381 (ppp) cc_final: 0.8144 (ppp) REVERT: A 1515 MET cc_start: 0.7822 (mtm) cc_final: 0.7603 (mtm) REVERT: A 1530 GLU cc_start: 0.8264 (tp30) cc_final: 0.7664 (tm-30) REVERT: A 1555 ASP cc_start: 0.8649 (m-30) cc_final: 0.8430 (t0) REVERT: A 1638 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8523 (tpp) REVERT: A 1650 MET cc_start: 0.7924 (mpp) cc_final: 0.7677 (mpp) REVERT: A 1717 MET cc_start: 0.9388 (tpp) cc_final: 0.9095 (tpp) REVERT: A 1747 MET cc_start: 0.8940 (mmp) cc_final: 0.8730 (mmm) REVERT: A 1928 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8841 (pttm) REVERT: A 2298 ASP cc_start: 0.8520 (m-30) cc_final: 0.7697 (m-30) REVERT: C 63 GLN cc_start: 0.7497 (mt0) cc_final: 0.7104 (mt0) REVERT: C 135 CYS cc_start: 0.7670 (t) cc_final: 0.7275 (t) REVERT: C 147 ASP cc_start: 0.8639 (p0) cc_final: 0.8145 (p0) REVERT: C 185 MET cc_start: 0.7255 (tmm) cc_final: 0.7052 (tmm) REVERT: C 195 TYR cc_start: 0.7249 (m-80) cc_final: 0.6896 (m-10) REVERT: E 81 TYR cc_start: 0.7830 (m-80) cc_final: 0.7556 (m-80) REVERT: E 124 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8174 (mmmm) REVERT: E 372 GLU cc_start: 0.8033 (tt0) cc_final: 0.7785 (pt0) REVERT: E 475 CYS cc_start: 0.8638 (m) cc_final: 0.8255 (m) REVERT: E 559 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7735 (t0) REVERT: E 696 HIS cc_start: 0.7358 (OUTLIER) cc_final: 0.6906 (p90) REVERT: E 1642 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8381 (tptt) REVERT: G 27 CYS cc_start: 0.9025 (m) cc_final: 0.8779 (m) REVERT: G 89 ARG cc_start: 0.9055 (mtp180) cc_final: 0.8254 (mtp180) REVERT: I 148 ASN cc_start: 0.7439 (t0) cc_final: 0.6744 (t0) REVERT: I 149 THR cc_start: 0.3587 (OUTLIER) cc_final: 0.3107 (p) REVERT: I 212 ASN cc_start: 0.9044 (p0) cc_final: 0.8800 (t0) REVERT: I 219 MET cc_start: 0.8578 (tpp) cc_final: 0.8202 (tmm) REVERT: I 228 MET cc_start: 0.4008 (tpt) cc_final: 0.3056 (mmt) REVERT: I 319 LEU cc_start: 0.8809 (tp) cc_final: 0.8525 (tp) REVERT: I 366 MET cc_start: 0.6031 (ttt) cc_final: 0.5808 (ttp) REVERT: I 376 ASN cc_start: 0.9037 (p0) cc_final: 0.8385 (m-40) outliers start: 80 outliers final: 36 residues processed: 536 average time/residue: 0.1883 time to fit residues: 165.2392 Evaluate side-chains 409 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 368 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1533 THR Chi-restraints excluded: chain A residue 1638 MET Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain E residue 1492 ILE Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 390 ASN Chi-restraints excluded: chain I residue 401 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 300 optimal weight: 0.9990 chunk 359 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 318 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 377 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 378 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 HIS A 752 GLN ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN A1758 GLN A1760 ASN A1806 HIS C 30 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 559 ASN ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067912 restraints weight = 97757.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070097 restraints weight = 47929.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071519 restraints weight = 30176.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072437 restraints weight = 22201.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073067 restraints weight = 18130.816| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31654 Z= 0.164 Angle : 0.608 11.338 42934 Z= 0.311 Chirality : 0.042 0.347 4953 Planarity : 0.004 0.071 5513 Dihedral : 4.670 59.315 4394 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.47 % Allowed : 12.96 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3977 helix: 0.83 (0.11), residues: 2424 sheet: -0.34 (0.37), residues: 198 loop : -1.08 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 94 TYR 0.028 0.002 TYR A2542 PHE 0.021 0.001 PHE E 611 TRP 0.029 0.001 TRP A1269 HIS 0.008 0.001 HIS A 743 Details of bonding type rmsd covalent geometry : bond 0.00365 (31649) covalent geometry : angle 0.60769 (42931) hydrogen bonds : bond 0.04882 ( 1592) hydrogen bonds : angle 4.34402 ( 4659) metal coordination : bond 0.02148 ( 4) metal coordination : angle 1.65627 ( 3) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 386 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9228 (t) cc_final: 0.8850 (t) REVERT: A 620 MET cc_start: 0.8299 (tpp) cc_final: 0.7838 (mmt) REVERT: A 630 LEU cc_start: 0.9117 (mt) cc_final: 0.8902 (tp) REVERT: A 671 ILE cc_start: 0.8476 (mm) cc_final: 0.8048 (mm) REVERT: A 679 LEU cc_start: 0.9438 (mm) cc_final: 0.9031 (mm) REVERT: A 772 MET cc_start: 0.8675 (mmt) cc_final: 0.8248 (mmm) REVERT: A 816 TRP cc_start: 0.8166 (m100) cc_final: 0.7776 (m100) REVERT: A 1154 ARG cc_start: 0.8534 (ttt180) cc_final: 0.8288 (ttt180) REVERT: A 1194 MET cc_start: 0.8834 (tmm) cc_final: 0.8411 (tmm) REVERT: A 1481 MET cc_start: 0.8070 (mmt) cc_final: 0.7795 (mmp) REVERT: A 1489 GLU cc_start: 0.8352 (mp0) cc_final: 0.8134 (mp0) REVERT: A 1530 GLU cc_start: 0.8365 (tp30) cc_final: 0.7674 (tm-30) REVERT: A 1555 ASP cc_start: 0.8881 (m-30) cc_final: 0.8663 (t0) REVERT: A 1650 MET cc_start: 0.8082 (mpp) cc_final: 0.7802 (mpp) REVERT: A 1701 MET cc_start: 0.9172 (mtm) cc_final: 0.8893 (mtm) REVERT: A 1704 MET cc_start: 0.8564 (ttm) cc_final: 0.8301 (ttm) REVERT: A 1711 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9288 (mp) REVERT: A 1717 MET cc_start: 0.9402 (tpp) cc_final: 0.9062 (tpp) REVERT: A 2014 GLU cc_start: 0.8280 (tp30) cc_final: 0.8066 (tp30) REVERT: A 2175 MET cc_start: 0.8804 (tpp) cc_final: 0.8555 (tpt) REVERT: A 2298 ASP cc_start: 0.8716 (m-30) cc_final: 0.7938 (m-30) REVERT: C 63 GLN cc_start: 0.7664 (mt0) cc_final: 0.7102 (mt0) REVERT: C 68 TYR cc_start: 0.7172 (m-80) cc_final: 0.6858 (m-80) REVERT: C 86 LYS cc_start: 0.7463 (mmmt) cc_final: 0.7123 (mmtp) REVERT: C 135 CYS cc_start: 0.7777 (t) cc_final: 0.7398 (t) REVERT: C 143 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6915 (mt) REVERT: C 147 ASP cc_start: 0.8678 (p0) cc_final: 0.8126 (p0) REVERT: C 185 MET cc_start: 0.7504 (tmm) cc_final: 0.7225 (tmm) REVERT: C 273 MET cc_start: 0.8045 (ttp) cc_final: 0.7840 (ttp) REVERT: E 81 TYR cc_start: 0.8112 (m-80) cc_final: 0.7751 (m-80) REVERT: E 124 LYS cc_start: 0.8462 (mmmt) cc_final: 0.7822 (mmmm) REVERT: E 372 GLU cc_start: 0.8464 (tt0) cc_final: 0.8045 (pt0) REVERT: E 504 THR cc_start: 0.8787 (m) cc_final: 0.8526 (p) REVERT: E 545 GLU cc_start: 0.6218 (tp30) cc_final: 0.5790 (tp30) REVERT: E 561 ASN cc_start: 0.6408 (p0) cc_final: 0.5696 (t0) REVERT: E 1642 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8313 (tptt) REVERT: G 21 SER cc_start: 0.8947 (m) cc_final: 0.8371 (t) REVERT: G 27 CYS cc_start: 0.9239 (m) cc_final: 0.8989 (m) REVERT: G 89 ARG cc_start: 0.9028 (mtp180) cc_final: 0.8740 (mmt180) REVERT: G 94 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8554 (ttp80) REVERT: I 134 MET cc_start: 0.9292 (ptt) cc_final: 0.8986 (mmm) REVERT: I 148 ASN cc_start: 0.7052 (t0) cc_final: 0.6517 (t0) REVERT: I 149 THR cc_start: 0.3821 (OUTLIER) cc_final: 0.1813 (p) REVERT: I 166 MET cc_start: 0.8926 (mmt) cc_final: 0.8470 (mmm) REVERT: I 194 MET cc_start: 0.8699 (ptp) cc_final: 0.8482 (ptt) REVERT: I 212 ASN cc_start: 0.8923 (p0) cc_final: 0.8652 (t0) REVERT: I 219 MET cc_start: 0.8641 (tpp) cc_final: 0.8433 (tmm) REVERT: I 228 MET cc_start: 0.4278 (tpt) cc_final: 0.3399 (mmt) REVERT: I 319 LEU cc_start: 0.8750 (tp) cc_final: 0.8485 (tp) REVERT: I 376 ASN cc_start: 0.9081 (p0) cc_final: 0.8444 (m-40) outliers start: 78 outliers final: 47 residues processed: 445 average time/residue: 0.1758 time to fit residues: 131.0220 Evaluate side-chains 388 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1505 ASN Chi-restraints excluded: chain A residue 1711 ILE Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2094 VAL Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 712 LEU Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 902 ILE Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain E residue 1663 CYS Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 393 LEU Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 196 optimal weight: 0.6980 chunk 1 optimal weight: 30.0000 chunk 250 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 400 optimal weight: 10.0000 chunk 384 optimal weight: 8.9990 chunk 12 optimal weight: 50.0000 chunk 178 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 372 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 539 GLN ** E 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 758 GLN G 105 ASN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.091689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065825 restraints weight = 98068.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067922 restraints weight = 48743.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069298 restraints weight = 31008.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070206 restraints weight = 22981.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070811 restraints weight = 18811.360| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31654 Z= 0.200 Angle : 0.622 10.696 42934 Z= 0.317 Chirality : 0.043 0.390 4953 Planarity : 0.004 0.046 5513 Dihedral : 4.603 56.999 4389 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.60 % Allowed : 14.80 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3977 helix: 0.97 (0.11), residues: 2424 sheet: -0.43 (0.36), residues: 203 loop : -1.07 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 386 TYR 0.028 0.002 TYR A2542 PHE 0.022 0.001 PHE E 611 TRP 0.025 0.001 TRP A2429 HIS 0.028 0.001 HIS A1806 Details of bonding type rmsd covalent geometry : bond 0.00452 (31649) covalent geometry : angle 0.62196 (42931) hydrogen bonds : bond 0.04529 ( 1592) hydrogen bonds : angle 4.29258 ( 4659) metal coordination : bond 0.02633 ( 4) metal coordination : angle 0.75924 ( 3) Misc. bond : bond 0.00111 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 344 time to evaluate : 1.218 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: A 606 CYS cc_start: 0.9272 (t) cc_final: 0.8902 (t) REVERT: A 620 MET cc_start: 0.8143 (tpp) cc_final: 0.7657 (mmt) REVERT: A 671 ILE cc_start: 0.8561 (mm) cc_final: 0.8110 (mm) REVERT: A 681 GLU cc_start: 0.8749 (tt0) cc_final: 0.8339 (mm-30) REVERT: A 772 MET cc_start: 0.8767 (mmt) cc_final: 0.8295 (mmp) REVERT: A 816 TRP cc_start: 0.8303 (m100) cc_final: 0.8085 (m100) REVERT: A 1154 ARG cc_start: 0.8593 (ttt180) cc_final: 0.8339 (ttt180) REVERT: A 1194 MET cc_start: 0.8933 (tmm) cc_final: 0.8450 (tmm) REVERT: A 1555 ASP cc_start: 0.8936 (m-30) cc_final: 0.8685 (t0) REVERT: A 1578 MET cc_start: 0.8349 (mmp) cc_final: 0.8089 (mtt) REVERT: A 1650 MET cc_start: 0.8093 (mpp) cc_final: 0.7798 (mpp) REVERT: A 1701 MET cc_start: 0.9169 (mtm) cc_final: 0.8936 (mtp) REVERT: A 1704 MET cc_start: 0.8530 (ttm) cc_final: 0.8240 (ttm) REVERT: A 1928 LYS cc_start: 0.9155 (pttm) cc_final: 0.8949 (pttm) REVERT: A 2014 GLU cc_start: 0.8350 (tp30) cc_final: 0.8058 (tp30) REVERT: C 68 TYR cc_start: 0.7295 (m-80) cc_final: 0.7069 (m-80) REVERT: C 143 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7017 (mt) REVERT: C 147 ASP cc_start: 0.8704 (p0) cc_final: 0.8132 (p0) REVERT: C 185 MET cc_start: 0.7690 (tmm) cc_final: 0.7084 (tmm) REVERT: C 273 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7820 (ttp) REVERT: C 307 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6988 (tm-30) REVERT: E 81 TYR cc_start: 0.8176 (m-80) cc_final: 0.7789 (m-80) REVERT: E 372 GLU cc_start: 0.8496 (tt0) cc_final: 0.8007 (pt0) REVERT: E 504 THR cc_start: 0.8895 (m) cc_final: 0.8632 (p) REVERT: E 561 ASN cc_start: 0.6483 (p0) cc_final: 0.5953 (t0) REVERT: E 1642 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8345 (tptt) REVERT: G 21 SER cc_start: 0.8918 (m) cc_final: 0.8342 (t) REVERT: I 134 MET cc_start: 0.9362 (ptt) cc_final: 0.9106 (mmm) REVERT: I 149 THR cc_start: 0.3834 (OUTLIER) cc_final: 0.3375 (p) REVERT: I 166 MET cc_start: 0.8969 (mmt) cc_final: 0.8503 (mmm) REVERT: I 194 MET cc_start: 0.8742 (ptp) cc_final: 0.8515 (ptt) REVERT: I 212 ASN cc_start: 0.8894 (p0) cc_final: 0.8635 (t0) REVERT: I 217 PHE cc_start: 0.8552 (m-80) cc_final: 0.8269 (m-10) REVERT: I 228 MET cc_start: 0.4378 (tpt) cc_final: 0.3480 (mmt) REVERT: I 319 LEU cc_start: 0.8761 (tp) cc_final: 0.8521 (tp) REVERT: I 326 TYR cc_start: 0.7189 (p90) cc_final: 0.6429 (p90) REVERT: I 376 ASN cc_start: 0.9133 (p0) cc_final: 0.8515 (m-40) outliers start: 82 outliers final: 54 residues processed: 404 average time/residue: 0.1716 time to fit residues: 115.8133 Evaluate side-chains 378 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 321 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1505 ASN Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2094 VAL Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain A residue 2387 MET Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 602 THR Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 744 VAL Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 902 ILE Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain E residue 1663 CYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 221 PHE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 146 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 196 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 385 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 337 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 394 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 ASN A1806 HIS C 30 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN E1662 HIS G 107 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.093934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068079 restraints weight = 97600.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070241 restraints weight = 47867.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.071652 restraints weight = 30185.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.072614 restraints weight = 22246.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.073235 restraints weight = 18026.881| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 31654 Z= 0.112 Angle : 0.560 11.877 42934 Z= 0.282 Chirality : 0.040 0.308 4953 Planarity : 0.003 0.043 5513 Dihedral : 4.509 57.951 4389 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.31 % Allowed : 16.03 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3977 helix: 1.15 (0.11), residues: 2429 sheet: -0.35 (0.37), residues: 203 loop : -1.09 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 563 TYR 0.030 0.001 TYR A2542 PHE 0.017 0.001 PHE E 611 TRP 0.030 0.001 TRP A2429 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00244 (31649) covalent geometry : angle 0.55969 (42931) hydrogen bonds : bond 0.03814 ( 1592) hydrogen bonds : angle 3.98573 ( 4659) metal coordination : bond 0.00417 ( 4) metal coordination : angle 0.90660 ( 3) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 364 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.5711 (tmm) cc_final: 0.5357 (tmm) REVERT: A 606 CYS cc_start: 0.9249 (t) cc_final: 0.8847 (t) REVERT: A 620 MET cc_start: 0.8144 (tpp) cc_final: 0.7716 (mmt) REVERT: A 671 ILE cc_start: 0.8532 (mm) cc_final: 0.7989 (mm) REVERT: A 729 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 768 ILE cc_start: 0.9021 (mm) cc_final: 0.8620 (tp) REVERT: A 772 MET cc_start: 0.8653 (mmt) cc_final: 0.8252 (mmp) REVERT: A 816 TRP cc_start: 0.8157 (m100) cc_final: 0.7610 (m100) REVERT: A 878 GLN cc_start: 0.6822 (tp40) cc_final: 0.6277 (tp40) REVERT: A 1154 ARG cc_start: 0.8566 (ttt180) cc_final: 0.8317 (ttt180) REVERT: A 1194 MET cc_start: 0.8901 (tmm) cc_final: 0.8457 (tmm) REVERT: A 1231 ILE cc_start: 0.9366 (tp) cc_final: 0.9135 (tp) REVERT: A 1313 MET cc_start: 0.8727 (ppp) cc_final: 0.8332 (tmm) REVERT: A 1555 ASP cc_start: 0.8895 (m-30) cc_final: 0.8610 (t0) REVERT: A 1559 LEU cc_start: 0.9089 (tp) cc_final: 0.8671 (mp) REVERT: A 1638 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8517 (tpp) REVERT: A 1650 MET cc_start: 0.8037 (mpp) cc_final: 0.7761 (mpp) REVERT: A 1704 MET cc_start: 0.8541 (ttm) cc_final: 0.8296 (ttm) REVERT: A 2014 GLU cc_start: 0.8358 (tp30) cc_final: 0.8043 (tp30) REVERT: A 2415 MET cc_start: 0.8788 (tpp) cc_final: 0.8455 (tpp) REVERT: C 63 GLN cc_start: 0.7737 (mt0) cc_final: 0.7147 (mt0) REVERT: C 143 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6784 (mp) REVERT: C 147 ASP cc_start: 0.8648 (p0) cc_final: 0.8056 (p0) REVERT: C 185 MET cc_start: 0.7572 (tmm) cc_final: 0.6991 (tmm) REVERT: E 124 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7909 (mmmm) REVERT: E 504 THR cc_start: 0.8927 (m) cc_final: 0.8694 (p) REVERT: E 561 ASN cc_start: 0.6535 (p0) cc_final: 0.5754 (t0) REVERT: E 696 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6725 (p90) REVERT: E 1642 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8313 (tptt) REVERT: G 21 SER cc_start: 0.8802 (m) cc_final: 0.8226 (t) REVERT: G 91 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8175 (tm-30) REVERT: G 95 LYS cc_start: 0.9337 (tppt) cc_final: 0.9080 (tppt) REVERT: I 134 MET cc_start: 0.9348 (ptt) cc_final: 0.9131 (mmm) REVERT: I 166 MET cc_start: 0.9060 (mmt) cc_final: 0.8705 (mmm) REVERT: I 212 ASN cc_start: 0.8847 (p0) cc_final: 0.8542 (t0) REVERT: I 228 MET cc_start: 0.4325 (tpt) cc_final: 0.3465 (mmt) REVERT: I 319 LEU cc_start: 0.8734 (tp) cc_final: 0.8417 (mm) REVERT: I 326 TYR cc_start: 0.7051 (p90) cc_final: 0.6245 (p90) REVERT: I 376 ASN cc_start: 0.9097 (p0) cc_final: 0.8497 (m-40) outliers start: 73 outliers final: 45 residues processed: 414 average time/residue: 0.1790 time to fit residues: 122.5379 Evaluate side-chains 375 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 326 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1638 MET Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 LEU Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 80 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 341 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 148 optimal weight: 0.4980 chunk 384 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 287 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN E 49 GLN ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 908 ASN G 107 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.093744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067952 restraints weight = 96997.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070122 restraints weight = 47650.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071530 restraints weight = 30017.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072471 restraints weight = 22127.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073071 restraints weight = 18007.669| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31654 Z= 0.118 Angle : 0.566 11.625 42934 Z= 0.283 Chirality : 0.040 0.333 4953 Planarity : 0.003 0.043 5513 Dihedral : 4.373 57.445 4386 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.63 % Allowed : 16.57 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3977 helix: 1.26 (0.11), residues: 2424 sheet: -0.30 (0.37), residues: 204 loop : -1.10 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 94 TYR 0.030 0.001 TYR A2542 PHE 0.024 0.001 PHE I 221 TRP 0.031 0.001 TRP A2429 HIS 0.019 0.001 HIS A1806 Details of bonding type rmsd covalent geometry : bond 0.00267 (31649) covalent geometry : angle 0.56590 (42931) hydrogen bonds : bond 0.03639 ( 1592) hydrogen bonds : angle 3.91503 ( 4659) metal coordination : bond 0.00692 ( 4) metal coordination : angle 0.70249 ( 3) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 341 time to evaluate : 1.253 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: A 606 CYS cc_start: 0.9226 (t) cc_final: 0.8845 (t) REVERT: A 620 MET cc_start: 0.8105 (tpp) cc_final: 0.7768 (mmt) REVERT: A 629 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7954 (mm) REVERT: A 700 LEU cc_start: 0.8541 (mp) cc_final: 0.8281 (mp) REVERT: A 729 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7621 (t80) REVERT: A 768 ILE cc_start: 0.9021 (mm) cc_final: 0.8564 (tp) REVERT: A 816 TRP cc_start: 0.8155 (m100) cc_final: 0.7605 (m100) REVERT: A 821 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8420 (t80) REVERT: A 853 TYR cc_start: 0.8419 (t80) cc_final: 0.7880 (t80) REVERT: A 1018 MET cc_start: 0.9214 (mmm) cc_final: 0.9003 (mmm) REVERT: A 1154 ARG cc_start: 0.8569 (ttt180) cc_final: 0.8328 (ttt180) REVERT: A 1194 MET cc_start: 0.8899 (tmm) cc_final: 0.8466 (tmm) REVERT: A 1291 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8615 (mm) REVERT: A 1313 MET cc_start: 0.8730 (ppp) cc_final: 0.8308 (tmm) REVERT: A 1530 GLU cc_start: 0.8344 (tp30) cc_final: 0.7609 (tm-30) REVERT: A 1555 ASP cc_start: 0.8886 (m-30) cc_final: 0.8601 (t0) REVERT: A 1578 MET cc_start: 0.8378 (mmp) cc_final: 0.8037 (mtt) REVERT: A 1638 MET cc_start: 0.8788 (ttp) cc_final: 0.8543 (tpp) REVERT: A 1650 MET cc_start: 0.8042 (mpp) cc_final: 0.7773 (mpp) REVERT: A 1704 MET cc_start: 0.8555 (ttm) cc_final: 0.8296 (ttm) REVERT: A 2014 GLU cc_start: 0.8345 (tp30) cc_final: 0.8014 (tp30) REVERT: A 2132 MET cc_start: 0.8092 (ptt) cc_final: 0.7830 (ptt) REVERT: C 143 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6689 (mp) REVERT: C 147 ASP cc_start: 0.8644 (p0) cc_final: 0.8048 (p0) REVERT: C 185 MET cc_start: 0.7609 (tmm) cc_final: 0.7017 (tmm) REVERT: C 307 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7005 (tm-30) REVERT: E 124 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7986 (mmmm) REVERT: E 126 ASP cc_start: 0.8910 (p0) cc_final: 0.8684 (p0) REVERT: E 504 THR cc_start: 0.8921 (m) cc_final: 0.8698 (p) REVERT: E 561 ASN cc_start: 0.6510 (p0) cc_final: 0.5921 (t0) REVERT: E 696 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.6752 (p90) REVERT: E 769 GLU cc_start: 0.8345 (tp30) cc_final: 0.8141 (tp30) REVERT: E 1642 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8311 (tptt) REVERT: G 21 SER cc_start: 0.8833 (m) cc_final: 0.8259 (t) REVERT: G 26 MET cc_start: 0.7560 (mmm) cc_final: 0.7332 (mmm) REVERT: I 134 MET cc_start: 0.9384 (ptt) cc_final: 0.9169 (mmm) REVERT: I 166 MET cc_start: 0.9067 (mmt) cc_final: 0.8728 (mmm) REVERT: I 193 LEU cc_start: 0.9205 (tt) cc_final: 0.8958 (mm) REVERT: I 194 MET cc_start: 0.8833 (ptp) cc_final: 0.8547 (ptt) REVERT: I 212 ASN cc_start: 0.8869 (p0) cc_final: 0.8582 (t0) REVERT: I 228 MET cc_start: 0.4468 (tpt) cc_final: 0.3584 (mmt) REVERT: I 319 LEU cc_start: 0.8796 (tp) cc_final: 0.8389 (mm) outliers start: 83 outliers final: 57 residues processed: 404 average time/residue: 0.1713 time to fit residues: 116.9532 Evaluate side-chains 382 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1754 LEU Chi-restraints excluded: chain A residue 1972 LEU Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2094 VAL Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 351 LEU Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain E residue 1663 CYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 44 optimal weight: 0.8980 chunk 377 optimal weight: 3.9990 chunk 324 optimal weight: 3.9990 chunk 400 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 0.0050 chunk 32 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 351 optimal weight: 6.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1806 HIS ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.093816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068119 restraints weight = 97269.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070289 restraints weight = 47609.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071733 restraints weight = 29959.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072689 restraints weight = 21902.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073299 restraints weight = 17755.280| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31654 Z= 0.113 Angle : 0.566 11.904 42934 Z= 0.282 Chirality : 0.040 0.345 4953 Planarity : 0.003 0.042 5513 Dihedral : 4.342 57.184 4386 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.57 % Allowed : 17.52 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3977 helix: 1.31 (0.11), residues: 2425 sheet: -0.22 (0.38), residues: 198 loop : -1.11 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 94 TYR 0.031 0.001 TYR A2542 PHE 0.013 0.001 PHE E 611 TRP 0.036 0.001 TRP A1269 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00256 (31649) covalent geometry : angle 0.56593 (42931) hydrogen bonds : bond 0.03490 ( 1592) hydrogen bonds : angle 3.87797 ( 4659) metal coordination : bond 0.00647 ( 4) metal coordination : angle 0.79888 ( 3) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 340 time to evaluate : 0.928 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: A 606 CYS cc_start: 0.9211 (t) cc_final: 0.8852 (t) REVERT: A 629 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8017 (mm) REVERT: A 729 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7646 (t80) REVERT: A 768 ILE cc_start: 0.8968 (mm) cc_final: 0.8732 (tp) REVERT: A 772 MET cc_start: 0.8629 (mmp) cc_final: 0.8368 (mmt) REVERT: A 816 TRP cc_start: 0.8165 (m100) cc_final: 0.7618 (m100) REVERT: A 853 TYR cc_start: 0.8343 (t80) cc_final: 0.7908 (t80) REVERT: A 878 GLN cc_start: 0.6837 (tp40) cc_final: 0.6308 (tp40) REVERT: A 1018 MET cc_start: 0.9201 (mmm) cc_final: 0.8997 (mmm) REVERT: A 1154 ARG cc_start: 0.8567 (ttt180) cc_final: 0.8308 (ttt180) REVERT: A 1171 SER cc_start: 0.8293 (m) cc_final: 0.7978 (p) REVERT: A 1194 MET cc_start: 0.8913 (tmm) cc_final: 0.8478 (tmm) REVERT: A 1231 ILE cc_start: 0.9304 (tp) cc_final: 0.8900 (tp) REVERT: A 1313 MET cc_start: 0.8632 (ppp) cc_final: 0.8250 (tmm) REVERT: A 1530 GLU cc_start: 0.8337 (tp30) cc_final: 0.7622 (tm-30) REVERT: A 1555 ASP cc_start: 0.8891 (m-30) cc_final: 0.8619 (t0) REVERT: A 1578 MET cc_start: 0.8449 (mmp) cc_final: 0.7975 (mtt) REVERT: A 1638 MET cc_start: 0.8809 (ttp) cc_final: 0.8524 (tpp) REVERT: A 1650 MET cc_start: 0.8004 (mpp) cc_final: 0.7757 (mpp) REVERT: A 1704 MET cc_start: 0.8547 (ttm) cc_final: 0.8289 (ttm) REVERT: A 1717 MET cc_start: 0.9402 (tpp) cc_final: 0.9193 (tpt) REVERT: A 2014 GLU cc_start: 0.8359 (tp30) cc_final: 0.8025 (tp30) REVERT: C 118 ASN cc_start: 0.8607 (t0) cc_final: 0.7997 (t0) REVERT: C 143 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6774 (mp) REVERT: C 147 ASP cc_start: 0.8624 (p0) cc_final: 0.8029 (p0) REVERT: E 124 LYS cc_start: 0.8487 (mmmt) cc_final: 0.7992 (mmmm) REVERT: E 126 ASP cc_start: 0.8948 (p0) cc_final: 0.8746 (p0) REVERT: E 351 LEU cc_start: 0.9093 (tp) cc_final: 0.8818 (mm) REVERT: E 504 THR cc_start: 0.8926 (m) cc_final: 0.8710 (p) REVERT: E 545 GLU cc_start: 0.6202 (tp30) cc_final: 0.5746 (tp30) REVERT: E 561 ASN cc_start: 0.6518 (p0) cc_final: 0.5939 (t0) REVERT: E 696 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6766 (p90) REVERT: E 769 GLU cc_start: 0.8330 (tp30) cc_final: 0.8127 (tp30) REVERT: E 1607 MET cc_start: 0.6123 (mmp) cc_final: 0.5788 (mmm) REVERT: E 1642 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8262 (tptt) REVERT: G 21 SER cc_start: 0.8825 (m) cc_final: 0.8234 (t) REVERT: I 193 LEU cc_start: 0.9179 (tt) cc_final: 0.8972 (mm) REVERT: I 194 MET cc_start: 0.8732 (ptp) cc_final: 0.8437 (ptt) REVERT: I 228 MET cc_start: 0.4458 (tpt) cc_final: 0.3606 (mmt) REVERT: I 326 TYR cc_start: 0.7029 (p90) cc_final: 0.6543 (p90) REVERT: I 376 ASN cc_start: 0.9269 (p0) cc_final: 0.8453 (m-40) outliers start: 81 outliers final: 57 residues processed: 405 average time/residue: 0.1648 time to fit residues: 113.2238 Evaluate side-chains 385 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1806 HIS Chi-restraints excluded: chain A residue 1972 LEU Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2094 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 902 ILE Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain E residue 1663 CYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 259 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 397 optimal weight: 0.0980 chunk 244 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 118 optimal weight: 0.6980 chunk 399 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1791 HIS ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.093908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068199 restraints weight = 97483.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070372 restraints weight = 47814.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071804 restraints weight = 30174.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072761 restraints weight = 22192.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073374 restraints weight = 18001.997| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31654 Z= 0.111 Angle : 0.583 12.282 42934 Z= 0.287 Chirality : 0.040 0.334 4953 Planarity : 0.003 0.043 5513 Dihedral : 4.280 56.881 4385 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.50 % Allowed : 17.97 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.14), residues: 3977 helix: 1.35 (0.11), residues: 2430 sheet: -0.24 (0.37), residues: 199 loop : -1.13 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 94 TYR 0.030 0.001 TYR A2542 PHE 0.012 0.001 PHE E 79 TRP 0.038 0.001 TRP A2429 HIS 0.024 0.001 HIS A1806 Details of bonding type rmsd covalent geometry : bond 0.00252 (31649) covalent geometry : angle 0.58294 (42931) hydrogen bonds : bond 0.03402 ( 1592) hydrogen bonds : angle 3.85672 ( 4659) metal coordination : bond 0.00422 ( 4) metal coordination : angle 0.84015 ( 3) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 349 time to evaluate : 1.186 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: A 606 CYS cc_start: 0.9206 (t) cc_final: 0.8841 (t) REVERT: A 620 MET cc_start: 0.8118 (mmm) cc_final: 0.7756 (mmt) REVERT: A 629 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7850 (mm) REVERT: A 729 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7602 (t80) REVERT: A 816 TRP cc_start: 0.8183 (m100) cc_final: 0.7638 (m100) REVERT: A 821 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8527 (t80) REVERT: A 853 TYR cc_start: 0.8324 (t80) cc_final: 0.7928 (t80) REVERT: A 1154 ARG cc_start: 0.8545 (ttt180) cc_final: 0.8314 (ttt180) REVERT: A 1171 SER cc_start: 0.8304 (m) cc_final: 0.7992 (p) REVERT: A 1194 MET cc_start: 0.8900 (tmm) cc_final: 0.8502 (tmm) REVERT: A 1231 ILE cc_start: 0.9356 (tp) cc_final: 0.8917 (tp) REVERT: A 1313 MET cc_start: 0.8685 (ppp) cc_final: 0.8302 (tmm) REVERT: A 1530 GLU cc_start: 0.8324 (tp30) cc_final: 0.7605 (tm-30) REVERT: A 1638 MET cc_start: 0.8813 (ttp) cc_final: 0.8530 (tpp) REVERT: A 1650 MET cc_start: 0.7997 (mpp) cc_final: 0.7751 (mpp) REVERT: A 1704 MET cc_start: 0.8537 (ttm) cc_final: 0.8304 (ttm) REVERT: A 2014 GLU cc_start: 0.8374 (tp30) cc_final: 0.8021 (tp30) REVERT: A 2079 MET cc_start: 0.7891 (ttm) cc_final: 0.7672 (ttm) REVERT: A 2275 TYR cc_start: 0.8852 (t80) cc_final: 0.8630 (t80) REVERT: A 2415 MET cc_start: 0.8704 (tpp) cc_final: 0.8496 (tpp) REVERT: C 118 ASN cc_start: 0.8603 (t0) cc_final: 0.8007 (t0) REVERT: C 143 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6742 (mp) REVERT: C 147 ASP cc_start: 0.8616 (p0) cc_final: 0.8014 (p0) REVERT: E 124 LYS cc_start: 0.8478 (mmmt) cc_final: 0.7986 (mmmm) REVERT: E 251 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: E 351 LEU cc_start: 0.9091 (tp) cc_final: 0.8819 (mm) REVERT: E 504 THR cc_start: 0.8918 (m) cc_final: 0.8709 (p) REVERT: E 545 GLU cc_start: 0.6212 (tp30) cc_final: 0.5759 (tp30) REVERT: E 561 ASN cc_start: 0.6536 (p0) cc_final: 0.5945 (t0) REVERT: E 696 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6773 (p90) REVERT: E 1487 MET cc_start: 0.8493 (pmm) cc_final: 0.7798 (pmm) REVERT: E 1642 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8250 (tptt) REVERT: G 5 ASP cc_start: 0.8454 (t0) cc_final: 0.8146 (m-30) REVERT: G 21 SER cc_start: 0.8830 (m) cc_final: 0.8263 (t) REVERT: G 26 MET cc_start: 0.7479 (mmm) cc_final: 0.7269 (mmm) REVERT: G 89 ARG cc_start: 0.8847 (mtp180) cc_final: 0.8420 (ptm160) REVERT: I 177 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7811 (pt0) REVERT: I 193 LEU cc_start: 0.9189 (tt) cc_final: 0.8983 (mm) REVERT: I 194 MET cc_start: 0.8803 (ptp) cc_final: 0.8573 (ptt) REVERT: I 228 MET cc_start: 0.4734 (tpt) cc_final: 0.3867 (mmt) REVERT: I 319 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8202 (mt) REVERT: I 326 TYR cc_start: 0.6943 (p90) cc_final: 0.6376 (p90) REVERT: I 376 ASN cc_start: 0.9291 (p0) cc_final: 0.8453 (m-40) outliers start: 79 outliers final: 52 residues processed: 408 average time/residue: 0.1680 time to fit residues: 115.5020 Evaluate side-chains 389 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 329 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1972 LEU Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2094 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 444 HIS Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 686 LEU Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 902 ILE Chi-restraints excluded: chain E residue 1492 ILE Chi-restraints excluded: chain E residue 1663 CYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 177 GLU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 351 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 387 optimal weight: 1.9990 chunk 322 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 374 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1077 HIS A1760 ASN ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.092210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066814 restraints weight = 98053.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068841 restraints weight = 50006.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.070189 restraints weight = 32253.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071081 restraints weight = 24096.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071665 restraints weight = 19755.807| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31654 Z= 0.151 Angle : 0.623 16.825 42934 Z= 0.305 Chirality : 0.042 0.354 4953 Planarity : 0.004 0.049 5513 Dihedral : 4.316 55.170 4384 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.38 % Allowed : 18.47 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3977 helix: 1.36 (0.11), residues: 2428 sheet: -0.27 (0.37), residues: 199 loop : -1.11 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 833 TYR 0.030 0.001 TYR A2542 PHE 0.013 0.001 PHE I 331 TRP 0.042 0.002 TRP A2429 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00343 (31649) covalent geometry : angle 0.62273 (42931) hydrogen bonds : bond 0.03685 ( 1592) hydrogen bonds : angle 3.96613 ( 4659) metal coordination : bond 0.01323 ( 4) metal coordination : angle 0.92102 ( 3) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 342 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 CYS cc_start: 0.9208 (t) cc_final: 0.8860 (t) REVERT: A 620 MET cc_start: 0.7988 (mmm) cc_final: 0.7705 (mmt) REVERT: A 629 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7935 (mm) REVERT: A 671 ILE cc_start: 0.8638 (mm) cc_final: 0.8247 (mm) REVERT: A 729 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7589 (t80) REVERT: A 772 MET cc_start: 0.8773 (mmt) cc_final: 0.8558 (mmp) REVERT: A 821 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8538 (t80) REVERT: A 853 TYR cc_start: 0.8451 (t80) cc_final: 0.8122 (t80) REVERT: A 878 GLN cc_start: 0.6930 (tp40) cc_final: 0.6317 (tp40) REVERT: A 1018 MET cc_start: 0.9162 (mmm) cc_final: 0.8894 (mpp) REVERT: A 1171 SER cc_start: 0.8243 (m) cc_final: 0.7930 (p) REVERT: A 1194 MET cc_start: 0.8925 (tmm) cc_final: 0.8521 (tmm) REVERT: A 1313 MET cc_start: 0.8719 (ppp) cc_final: 0.8329 (tmm) REVERT: A 1467 MET cc_start: 0.8158 (mmp) cc_final: 0.7764 (mmm) REVERT: A 1530 GLU cc_start: 0.8358 (tp30) cc_final: 0.7666 (tm-30) REVERT: A 1578 MET cc_start: 0.8529 (mmp) cc_final: 0.8260 (mmm) REVERT: A 1650 MET cc_start: 0.8020 (mpp) cc_final: 0.7786 (mpp) REVERT: A 1704 MET cc_start: 0.8587 (ttm) cc_final: 0.8327 (ttm) REVERT: A 2014 GLU cc_start: 0.8393 (tp30) cc_final: 0.8055 (tp30) REVERT: A 2079 MET cc_start: 0.7885 (ttm) cc_final: 0.7670 (ttm) REVERT: A 2132 MET cc_start: 0.7993 (ptt) cc_final: 0.7689 (ptt) REVERT: A 2415 MET cc_start: 0.8713 (tpp) cc_final: 0.8495 (tpp) REVERT: A 2516 ASP cc_start: 0.8387 (m-30) cc_final: 0.7549 (p0) REVERT: C 118 ASN cc_start: 0.8627 (t0) cc_final: 0.8017 (t0) REVERT: C 143 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6890 (mp) REVERT: C 147 ASP cc_start: 0.8621 (p0) cc_final: 0.8045 (p0) REVERT: C 257 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 258 LEU cc_start: 0.7861 (mp) cc_final: 0.7415 (tt) REVERT: E 504 THR cc_start: 0.8986 (m) cc_final: 0.8775 (p) REVERT: E 545 GLU cc_start: 0.6186 (tp30) cc_final: 0.5777 (tp30) REVERT: E 561 ASN cc_start: 0.6721 (p0) cc_final: 0.6093 (t0) REVERT: E 696 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6759 (p90) REVERT: E 1642 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8275 (tptt) REVERT: G 5 ASP cc_start: 0.8468 (t0) cc_final: 0.8128 (m-30) REVERT: G 21 SER cc_start: 0.8856 (m) cc_final: 0.8323 (t) REVERT: G 33 ASP cc_start: 0.8113 (p0) cc_final: 0.7874 (p0) REVERT: G 89 ARG cc_start: 0.8838 (mtp180) cc_final: 0.8377 (ptm160) REVERT: I 193 LEU cc_start: 0.9185 (tt) cc_final: 0.8963 (mm) REVERT: I 228 MET cc_start: 0.4850 (tpt) cc_final: 0.3917 (mmt) REVERT: I 326 TYR cc_start: 0.6888 (p90) cc_final: 0.6501 (p90) REVERT: I 376 ASN cc_start: 0.9286 (p0) cc_final: 0.8443 (m-40) outliers start: 75 outliers final: 62 residues processed: 399 average time/residue: 0.1736 time to fit residues: 115.9006 Evaluate side-chains 399 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 332 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1505 ASN Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1976 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2094 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 686 LEU Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 894 HIS Chi-restraints excluded: chain E residue 902 ILE Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain E residue 1492 ILE Chi-restraints excluded: chain E residue 1663 CYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 380 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 282 optimal weight: 0.2980 chunk 253 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 399 optimal weight: 6.9990 chunk 323 optimal weight: 0.4980 chunk 286 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1509 GLN ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN ** E1674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.093432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.067858 restraints weight = 97220.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070015 restraints weight = 47803.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.071444 restraints weight = 30162.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072367 restraints weight = 22140.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.072981 restraints weight = 17999.175| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31654 Z= 0.115 Angle : 0.620 15.973 42934 Z= 0.301 Chirality : 0.041 0.403 4953 Planarity : 0.003 0.062 5513 Dihedral : 4.268 55.437 4384 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.19 % Allowed : 18.82 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3977 helix: 1.41 (0.11), residues: 2420 sheet: -0.13 (0.38), residues: 199 loop : -1.10 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 833 TYR 0.030 0.001 TYR A2542 PHE 0.017 0.001 PHE E 608 TRP 0.044 0.001 TRP I 173 HIS 0.004 0.001 HIS A1806 Details of bonding type rmsd covalent geometry : bond 0.00262 (31649) covalent geometry : angle 0.61948 (42931) hydrogen bonds : bond 0.03440 ( 1592) hydrogen bonds : angle 3.88978 ( 4659) metal coordination : bond 0.00343 ( 4) metal coordination : angle 0.92121 ( 3) Misc. bond : bond 0.00025 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7954 Ramachandran restraints generated. 3977 Oldfield, 0 Emsley, 3977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 348 time to evaluate : 1.076 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 606 CYS cc_start: 0.9222 (t) cc_final: 0.8885 (t) REVERT: A 620 MET cc_start: 0.8037 (mmm) cc_final: 0.7740 (mmt) REVERT: A 629 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7956 (mm) REVERT: A 671 ILE cc_start: 0.8629 (mm) cc_final: 0.8253 (mm) REVERT: A 679 LEU cc_start: 0.9401 (mm) cc_final: 0.8983 (mm) REVERT: A 729 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7574 (t80) REVERT: A 772 MET cc_start: 0.8757 (mmt) cc_final: 0.8526 (mmp) REVERT: A 816 TRP cc_start: 0.8208 (m100) cc_final: 0.7739 (m100) REVERT: A 821 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8514 (t80) REVERT: A 853 TYR cc_start: 0.8355 (t80) cc_final: 0.7976 (t80) REVERT: A 1018 MET cc_start: 0.9127 (mmm) cc_final: 0.8841 (mpp) REVERT: A 1171 SER cc_start: 0.8197 (m) cc_final: 0.7890 (p) REVERT: A 1194 MET cc_start: 0.8918 (tmm) cc_final: 0.8511 (tmm) REVERT: A 1313 MET cc_start: 0.8702 (ppp) cc_final: 0.8350 (tmm) REVERT: A 1467 MET cc_start: 0.8146 (mmp) cc_final: 0.7755 (mmm) REVERT: A 1530 GLU cc_start: 0.8320 (tp30) cc_final: 0.7614 (tm-30) REVERT: A 1578 MET cc_start: 0.8592 (mmp) cc_final: 0.8251 (mmm) REVERT: A 1638 MET cc_start: 0.8841 (ttp) cc_final: 0.8542 (tpp) REVERT: A 1650 MET cc_start: 0.7986 (mpp) cc_final: 0.7750 (mpp) REVERT: A 1704 MET cc_start: 0.8584 (ttm) cc_final: 0.8379 (ttm) REVERT: A 2014 GLU cc_start: 0.8361 (tp30) cc_final: 0.8018 (tp30) REVERT: A 2079 MET cc_start: 0.7884 (ttm) cc_final: 0.7668 (ttm) REVERT: A 2132 MET cc_start: 0.7974 (ptt) cc_final: 0.7681 (ptt) REVERT: A 2415 MET cc_start: 0.8685 (tpp) cc_final: 0.8471 (tpp) REVERT: A 2516 ASP cc_start: 0.8426 (m-30) cc_final: 0.7520 (p0) REVERT: C 118 ASN cc_start: 0.8586 (t0) cc_final: 0.8012 (t0) REVERT: C 143 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6823 (mp) REVERT: C 147 ASP cc_start: 0.8595 (p0) cc_final: 0.8000 (p0) REVERT: C 258 LEU cc_start: 0.7828 (mp) cc_final: 0.7356 (tt) REVERT: E 251 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: E 414 ASN cc_start: 0.8087 (t0) cc_final: 0.7528 (t0) REVERT: E 504 THR cc_start: 0.8982 (m) cc_final: 0.8767 (p) REVERT: E 545 GLU cc_start: 0.6195 (tp30) cc_final: 0.5773 (tp30) REVERT: E 561 ASN cc_start: 0.6794 (p0) cc_final: 0.6128 (t0) REVERT: E 696 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6712 (p90) REVERT: E 833 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7383 (ptp-170) REVERT: E 1642 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8260 (tptt) REVERT: G 5 ASP cc_start: 0.8488 (t0) cc_final: 0.8181 (m-30) REVERT: G 21 SER cc_start: 0.8821 (m) cc_final: 0.8282 (t) REVERT: G 89 ARG cc_start: 0.8845 (mtp180) cc_final: 0.8469 (ptm160) REVERT: I 134 MET cc_start: 0.9340 (ptt) cc_final: 0.9112 (mmm) REVERT: I 193 LEU cc_start: 0.9160 (tt) cc_final: 0.8950 (mm) REVERT: I 228 MET cc_start: 0.5033 (tpt) cc_final: 0.4123 (mmt) REVERT: I 326 TYR cc_start: 0.6898 (p90) cc_final: 0.6484 (p90) REVERT: I 376 ASN cc_start: 0.9301 (p0) cc_final: 0.8476 (m-40) outliers start: 69 outliers final: 56 residues processed: 399 average time/residue: 0.1743 time to fit residues: 116.9342 Evaluate side-chains 396 residues out of total 3575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 334 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1236 MET Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1593 CYS Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1724 MET Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1983 THR Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2094 VAL Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2228 ILE Chi-restraints excluded: chain A residue 2329 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 64 HIS Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 247 TRP Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 607 GLN Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 686 LEU Chi-restraints excluded: chain E residue 696 HIS Chi-restraints excluded: chain E residue 778 CYS Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 902 ILE Chi-restraints excluded: chain E residue 915 ASP Chi-restraints excluded: chain E residue 1492 ILE Chi-restraints excluded: chain E residue 1663 CYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 218 ARG Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 309 VAL Chi-restraints excluded: chain I residue 383 VAL Chi-restraints excluded: chain I residue 403 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 401 random chunks: chunk 360 optimal weight: 0.0270 chunk 372 optimal weight: 0.9990 chunk 357 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 332 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 351 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 GLN ** E1674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1684 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068256 restraints weight = 97612.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070431 restraints weight = 47861.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071862 restraints weight = 30104.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072801 restraints weight = 22061.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073396 restraints weight = 17912.831| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31654 Z= 0.111 Angle : 0.614 15.792 42934 Z= 0.297 Chirality : 0.041 0.396 4953 Planarity : 0.003 0.059 5513 Dihedral : 4.229 55.107 4384 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.06 % Allowed : 18.88 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3977 helix: 1.46 (0.11), residues: 2429 sheet: -0.06 (0.38), residues: 198 loop : -1.06 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 833 TYR 0.031 0.001 TYR A2542 PHE 0.028 0.001 PHE E 608 TRP 0.043 0.001 TRP A2429 HIS 0.004 0.001 HIS E 418 Details of bonding type rmsd covalent geometry : bond 0.00254 (31649) covalent geometry : angle 0.61439 (42931) hydrogen bonds : bond 0.03301 ( 1592) hydrogen bonds : angle 3.83642 ( 4659) metal coordination : bond 0.00234 ( 4) metal coordination : angle 0.95974 ( 3) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6056.23 seconds wall clock time: 104 minutes 49.77 seconds (6289.77 seconds total)