Starting phenix.real_space_refine on Sun Aug 9 04:29:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygq_72938/08_2026/9ygq_72938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygq_72938/08_2026/9ygq_72938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ygq_72938/08_2026/9ygq_72938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygq_72938/08_2026/9ygq_72938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ygq_72938/08_2026/9ygq_72938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygq_72938/08_2026/9ygq_72938.map" } resolution = 3.6 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= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 188 5.16 5 C 20003 2.51 5 N 5120 2.21 5 O 6110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31421 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9154 Classifications: {'peptide': 1179} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 49, 'TRANS': 1126} Chain breaks: 4 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 9243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9243 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 3, 'PTRANS': 50, 'TRANS': 1140} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 9254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9254 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 50, 'TRANS': 1140} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'PHE:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 804 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Restraints were copied for chains: I, M Time building chain proxies: 7.46, per 1000 atoms: 0.24 Number of scatterers: 31421 At special positions: 0 Unit cell: (149.96, 155.48, 219.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 188 16.00 O 6110 8.00 N 5120 7.00 C 20003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=67, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=1.29 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.04 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=1.29 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.02 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1401 " - " ASN A 58 " " NAG A1402 " - " ASN A 132 " " NAG A1403 " - " ASN A 188 " " NAG A1404 " - " ASN A 192 " " NAG A1405 " - " ASN A 664 " " NAG A1406 " - " ASN A 725 " " NAG A1407 " - " ASN A 793 " " NAG A1408 " - " ASN A 924 " " NAG A1409 " - " ASN A1211 " " NAG B1401 " - " ASN B 58 " " NAG B1402 " - " ASN B 335 " " NAG B1403 " - " ASN B 664 " " NAG B1404 " - " ASN B 725 " " NAG B1405 " - " ASN B 793 " " NAG B1406 " - " ASN B 924 " " NAG B1407 " - " ASN B1211 " " NAG C1401 " - " ASN C 58 " " NAG C1402 " - " ASN C 664 " " NAG C1403 " - " ASN C 725 " " NAG C1404 " - " ASN C 776 " " NAG C1405 " - " ASN C 793 " " NAG C1406 " - " ASN C 924 " Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7562 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 79 sheets defined 21.7% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.843A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.575A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 443 through 448 removed outlier: 4.003A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.517A pdb=" N VAL A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 483' Processing helix chain 'A' and resid 553 through 556 removed outlier: 3.748A pdb=" N CYS A 556 " --> pdb=" O GLU A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 813 through 818 removed outlier: 3.824A pdb=" N VAL A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.580A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 862 Processing helix chain 'A' and resid 885 through 888 Processing helix chain 'A' and resid 901 through 911 removed outlier: 4.161A pdb=" N VAL A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 924 removed outlier: 3.764A pdb=" N ASN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.557A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.536A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 removed outlier: 4.134A pdb=" N GLY A 989 " --> pdb=" O TYR A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.762A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1021 removed outlier: 3.547A pdb=" N ALA A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1046 removed outlier: 3.535A pdb=" N ALA A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1049 No H-bonds generated for 'chain 'A' and resid 1047 through 1049' Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.560A pdb=" N ILE A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.847A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A1111 " --> pdb=" O ILE A1107 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A1112 " --> pdb=" O GLU A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1183 removed outlier: 3.568A pdb=" N ASP A1182 " --> pdb=" O LYS A1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.522A pdb=" N TRP B 89 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.517A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.592A pdb=" N GLY B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 813 through 818 Processing helix chain 'B' and resid 822 through 828 removed outlier: 3.849A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 840 Processing helix chain 'B' and resid 841 through 862 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 4.323A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 909 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 4.255A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 951 through 964 Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 971 through 975 removed outlier: 3.570A pdb=" N ALA B 975 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 991 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.692A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1020 Processing helix chain 'B' and resid 1023 through 1046 Processing helix chain 'B' and resid 1057 through 1065 Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 4.884A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B1101 " --> pdb=" O THR B1097 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B1102 " --> pdb=" O LEU B1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.517A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 445 through 449 removed outlier: 3.592A pdb=" N GLY C 449 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 703 Processing helix chain 'C' and resid 781 through 785 Processing helix chain 'C' and resid 822 through 831 removed outlier: 3.526A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 861 removed outlier: 3.809A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 861 " --> pdb=" O VAL C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 911 Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.870A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR C 926 " --> pdb=" O TYR C 922 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY C 928 " --> pdb=" O ASN C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 4.237A pdb=" N VAL C 937 " --> pdb=" O ASP C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.647A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1021 Processing helix chain 'C' and resid 1023 through 1046 removed outlier: 3.548A pdb=" N ILE C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1057 through 1063 removed outlier: 3.678A pdb=" N ILE C1061 " --> pdb=" O SER C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 4.618A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.640A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.641A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 68 removed outlier: 3.501A pdb=" N LEU A 261 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE A 209 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER A 225 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA A 211 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 113 Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 190 removed outlier: 3.803A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR A 123 " --> pdb=" O MET A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 removed outlier: 3.512A pdb=" N SER A 173 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 160 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N HIS A 175 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 10.948A pdb=" N TYR A 158 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.623A pdb=" N GLY A 302 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 678 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA9, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.563A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.563A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.805A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 506 Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.585A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 632 through 635 removed outlier: 4.153A pdb=" N TYR A 667 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 658 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 731 removed outlier: 4.224A pdb=" N LEU A 736 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.106A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 794 through 799 removed outlier: 3.547A pdb=" N LEU A1141 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 803 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 794 through 799 removed outlier: 3.507A pdb=" N GLY A1140 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A1137 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A1146 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 867 through 868 removed outlier: 7.274A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 878 through 879 removed outlier: 3.711A pdb=" N VAL A 879 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.530A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 1175 through 1178 Processing sheet with id=AC7, first strand: chain 'B' and resid 59 through 67 removed outlier: 7.757A pdb=" N GLN B 265 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASP B 281 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.525A pdb=" N ARG B 75 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 257 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 211 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 96 through 97 removed outlier: 4.012A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 109 through 113 Processing sheet with id=AD2, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.646A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 305 removed outlier: 3.673A pdb=" N GLY B 302 " --> pdb=" O PHE B 681 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 681 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 316 through 319 removed outlier: 7.010A pdb=" N VAL B 317 " --> pdb=" O ASP B 623 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AD6, first strand: chain 'B' and resid 345 through 350 removed outlier: 3.572A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AD8, first strand: chain 'B' and resid 459 through 463 removed outlier: 3.549A pdb=" N ASP B 578 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AE1, first strand: chain 'B' and resid 505 through 506 removed outlier: 3.500A pdb=" N ARG B 517 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 522 through 523 removed outlier: 4.400A pdb=" N ASP B 523 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE4, first strand: chain 'B' and resid 647 through 649 removed outlier: 6.486A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 691 through 693 removed outlier: 3.604A pdb=" N VAL B 720 " --> pdb=" O PHE B 713 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B 713 " --> pdb=" O VAL B 720 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 725 through 731 removed outlier: 11.692A pdb=" N TYR B 762 " --> pdb=" O ASN B 725 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N THR B 727 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE B 764 " --> pdb=" O THR B 727 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR B 729 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 766 " --> pdb=" O TYR B 729 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 786 through 791 removed outlier: 6.714A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B1176 " --> pdb=" O THR B1187 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B1187 " --> pdb=" O TYR B1176 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B1186 " --> pdb=" O GLU B1195 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY B1188 " --> pdb=" O TYR B1193 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 794 through 804 removed outlier: 3.920A pdb=" N ILE B 803 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B1141 " --> pdb=" O ILE B 803 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 809 through 811 removed outlier: 4.270A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 866 through 868 removed outlier: 6.548A pdb=" N LEU B 867 " --> pdb=" O VAL C 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 1162 through 1164 Processing sheet with id=AF3, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF4, first strand: chain 'C' and resid 62 through 67 Processing sheet with id=AF5, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.786A pdb=" N ARG C 75 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE C 209 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER C 225 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA C 211 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.103A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 148 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS C 187 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.276A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 302 through 306 removed outlier: 3.658A pdb=" N LEU C 690 " --> pdb=" O LEU C 721 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 721 " --> pdb=" O LEU C 690 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 316 through 317 Processing sheet with id=AG1, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AG2, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.732A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 382 through 383 Processing sheet with id=AG4, first strand: chain 'C' and resid 459 through 463 removed outlier: 3.549A pdb=" N ASP C 578 " --> pdb=" O VAL C 460 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 467 through 468 Processing sheet with id=AG6, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.500A pdb=" N ARG C 517 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 522 through 523 removed outlier: 4.400A pdb=" N ASP C 523 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AG9, first strand: chain 'C' and resid 635 through 636 removed outlier: 4.081A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 730 through 731 removed outlier: 4.271A pdb=" N VAL C 731 " --> pdb=" O THR C 766 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 786 through 790 Processing sheet with id=AH3, first strand: chain 'C' and resid 794 through 797 Processing sheet with id=AH4, first strand: chain 'C' and resid 794 through 797 removed outlier: 6.211A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 1202 through 1204 removed outlier: 3.967A pdb=" N VAL C1203 " --> pdb=" O ALA C1171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C1171 " --> pdb=" O VAL C1203 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE C1170 " --> pdb=" O LEU C1162 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU C1162 " --> pdb=" O ILE C1170 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 1177 through 1179 removed outlier: 3.531A pdb=" N ILE C1178 " --> pdb=" O MET C1185 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.641A pdb=" N LYS H 5 " --> pdb=" O ASN H 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 7 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS H 22 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR H 68 " --> pdb=" O THR H 81 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.773A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL H 35A" --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR H 94 " --> pdb=" O HIS H 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS H 102 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.641A pdb=" N LYS I 5 " --> pdb=" O ASN I 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER I 7 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS I 22 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR I 81 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR I 68 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.773A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU I 50 " --> pdb=" O VAL I 35A" (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL I 35A" --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR I 94 " --> pdb=" O HIS I 102 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS I 102 " --> pdb=" O TYR I 94 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.725A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.725A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 75 " --> pdb=" O VAL M 19 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU M 11 " --> pdb=" O ASP M 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE M 48 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU M 11 " --> pdb=" O ASP M 105 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 2868 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: 8.25 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8192 1.33 - 1.45: 6542 1.45 - 1.57: 17213 1.57 - 1.70: 0 1.70 - 1.82: 223 Bond restraints: 32170 Sorted by residual: bond pdb=" C SER A1094 " pdb=" O SER A1094 " ideal model delta sigma weight residual 1.237 1.276 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" N ILE B 656 " pdb=" CA ILE B 656 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.07e-02 8.73e+03 1.09e+01 bond pdb=" N ILE C 581 " pdb=" CA ILE C 581 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N ILE B 581 " pdb=" CA ILE B 581 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.08e+01 bond pdb=" N ILE C 436 " pdb=" CA ILE C 436 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.14e-02 7.69e+03 1.07e+01 ... (remaining 32165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 42417 1.73 - 3.47: 1276 3.47 - 5.20: 127 5.20 - 6.94: 22 6.94 - 8.67: 4 Bond angle restraints: 43846 Sorted by residual: angle pdb=" N LEU B1026 " pdb=" CA LEU B1026 " pdb=" C LEU B1026 " ideal model delta sigma weight residual 111.75 105.40 6.35 1.28e+00 6.10e-01 2.46e+01 angle pdb=" N ILE B 656 " pdb=" CA ILE B 656 " pdb=" C ILE B 656 " ideal model delta sigma weight residual 113.10 108.64 4.46 9.70e-01 1.06e+00 2.11e+01 angle pdb=" C VAL B1032 " pdb=" N VAL B1033 " pdb=" CA VAL B1033 " ideal model delta sigma weight residual 121.34 114.16 7.18 1.62e+00 3.81e-01 1.97e+01 angle pdb=" N ARG C 398 " pdb=" CA ARG C 398 " pdb=" C ARG C 398 " ideal model delta sigma weight residual 111.33 106.02 5.31 1.21e+00 6.83e-01 1.93e+01 angle pdb=" N ARG B 398 " pdb=" CA ARG B 398 " pdb=" C ARG B 398 " ideal model delta sigma weight residual 111.33 106.03 5.30 1.21e+00 6.83e-01 1.92e+01 ... (remaining 43841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 18677 17.57 - 35.14: 613 35.14 - 52.70: 114 52.70 - 70.27: 24 70.27 - 87.84: 3 Dihedral angle restraints: 19431 sinusoidal: 7651 harmonic: 11780 Sorted by residual: dihedral pdb=" CB CYS B 151 " pdb=" SG CYS B 151 " pdb=" SG CYS B 183 " pdb=" CB CYS B 183 " ideal model delta sinusoidal sigma weight residual -86.00 -55.08 -30.92 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CA SER L 94 " pdb=" C SER L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA SER M 94 " pdb=" C SER M 94 " pdb=" N PRO M 95 " pdb=" CA PRO M 95 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 19428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4516 0.084 - 0.169: 478 0.169 - 0.253: 37 0.253 - 0.337: 5 0.337 - 0.422: 1 Chirality restraints: 5037 Sorted by residual: chirality pdb=" C1 NAG C1406 " pdb=" ND2 ASN C 924 " pdb=" C2 NAG C1406 " pdb=" O5 NAG C1406 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" C1 NAG C1401 " pdb=" ND2 ASN C 58 " pdb=" C2 NAG C1401 " pdb=" O5 NAG C1401 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG B1404 " pdb=" ND2 ASN B 725 " pdb=" C2 NAG B1404 " pdb=" O5 NAG B1404 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 5034 not shown) Planarity restraints: 5632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1404 " -0.201 2.00e-02 2.50e+03 1.69e-01 3.57e+02 pdb=" C7 NAG B1404 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG B1404 " -0.143 2.00e-02 2.50e+03 pdb=" N2 NAG B1404 " 0.281 2.00e-02 2.50e+03 pdb=" O7 NAG B1404 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1403 " 0.199 2.00e-02 2.50e+03 1.65e-01 3.40e+02 pdb=" C7 NAG C1403 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG C1403 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG C1403 " -0.266 2.00e-02 2.50e+03 pdb=" O7 NAG C1403 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1404 " -0.186 2.00e-02 2.50e+03 1.59e-01 3.17e+02 pdb=" C7 NAG A1404 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG A1404 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG A1404 " 0.264 2.00e-02 2.50e+03 pdb=" O7 NAG A1404 " -0.143 2.00e-02 2.50e+03 ... (remaining 5629 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 264 2.61 - 3.18: 26584 3.18 - 3.75: 47273 3.75 - 4.33: 65116 4.33 - 4.90: 107446 Nonbonded interactions: 246683 Sorted by model distance: nonbonded pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.036 3.760 nonbonded pdb=" O VAL A 113 " pdb=" OG1 THR A 116 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR A 792 " pdb=" OG SER A1152 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR C 123 " pdb=" O VAL C 139 " model vdw 2.271 3.040 ... (remaining 246678 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 90 or (resid 91 and (name N or nam \ e CA or name C or name O or name CB )) or resid 92 through 344 or (resid 345 thr \ ough 346 and (name N or name CA or name C or name O or name CB )) or resid 347 t \ hrough 360 or (resid 361 and (name N or name CA or name C or name O or name CB ) \ ) or resid 362 through 378 or (resid 379 and (name N or name CA or name C or nam \ e O or name CB )) or resid 380 through 389 or (resid 390 and (name N or name CA \ or name C or name O or name CB )) or resid 391 through 499 or (resid 500 and (na \ me N or name CA or name C or name O or name CB )) or resid 501 through 626 or (r \ esid 627 and (name N or name CA or name C or name O or name CB )) or resid 628 t \ hrough 708 or (resid 709 and (name N or name CA or name C or name O or name CB ) \ ) or resid 710 through 779 or (resid 780 and (name N or name CA or name C or nam \ e O or name CB )) or resid 781 through 836 or (resid 837 and (name N or name CA \ or name C or name O or name CB )) or resid 838 through 875 or (resid 876 and (na \ me N or name CA or name C or name O or name CB )) or resid 877 through 929 or (r \ esid 930 through 932 and (name N or name CA or name C or name O or name CB )) or \ resid 933 through 998 or (resid 999 and (name N or name CA or name C or name O \ or name CB )) or resid 1000 through 1065 or (resid 1066 and (name N or name CA o \ r name C or name O or name CB )) or resid 1067 through 1148 or (resid 1149 and ( \ name N or name CA or name C or name O or name CB )) or resid 1150 through 1199 o \ r (resid 1200 and (name N or name CA or name C or name O or name CB )) or resid \ 1201 through 1406)) selection = (chain 'B' and (resid 14 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 68 or (resid 69 and (name N or nam \ e CA or name C or name O or name CB )) or resid 70 through 232 or (resid 233 and \ (name N or name CA or name C or name O or name CB )) or resid 234 through 246 o \ r (resid 247 through 248 and (name N or name CA or name C or name O or name CB ) \ ) or resid 249 or (resid 250 through 253 and (name N or name CA or name C or nam \ e O or name CB )) or resid 254 through 308 or resid 317 through 626 or (resid 62 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 628 through \ 629 or (resid 630 and (name N or name CA or name C or name O or name CB )) or re \ sid 631 through 705 or (resid 706 and (name N or name CA or name C or name O or \ name CB )) or resid 707 through 708 or (resid 709 and (name N or name CA or name \ C or name O or name CB )) or resid 710 through 779 or (resid 780 and (name N or \ name CA or name C or name O or name CB )) or resid 781 through 836 or (resid 83 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 838 through \ 890 or (resid 891 and (name N or name CA or name C or name O or name CB )) or re \ sid 899 through 998 or (resid 999 and (name N or name CA or name C or name O or \ name CB )) or resid 1000 through 1199 or (resid 1200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1201 through 1406)) selection = (chain 'C' and (resid 14 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 90 or (r \ esid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 232 or (resid 233 and (name N or name CA or name C or name O or name CB )) \ or resid 234 through 246 or (resid 247 through 248 and (name N or name CA or nam \ e C or name O or name CB )) or resid 249 or (resid 250 through 253 and (name N o \ r name CA or name C or name O or name CB )) or resid 254 through 308 or resid 31 \ 7 through 615 or (resid 616 and (name N or name CA or name C or name O or name C \ B )) or resid 617 through 619 or (resid 620 and (name N or name CA or name C or \ name O or name CB )) or resid 621 through 629 or (resid 630 and (name N or name \ CA or name C or name O or name CB )) or resid 631 or (resid 632 and (name N or n \ ame CA or name C or name O or name CB )) or resid 633 or (resid 634 and (name N \ or name CA or name C or name O or name CB )) or resid 635 through 651 or (resid \ 652 and (name N or name CA or name C or name O or name CB )) or resid 653 or (re \ sid 654 and (name N or name CA or name C or name O or name CB )) or resid 655 th \ rough 875 or (resid 876 and (name N or name CA or name C or name O or name CB )) \ or resid 877 through 890 or (resid 891 and (name N or name CA or name C or name \ O or name CB )) or resid 899 through 930 or (resid 931 through 932 and (name N \ or name CA or name C or name O or name CB )) or resid 933 through 1065 or (resid \ 1066 and (name N or name CA or name C or name O or name CB )) or resid 1067 thr \ ough 1148 or (resid 1149 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1150 through 1406)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } 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: 7.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.430 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4454 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 : 0.007 0.742 32259 Z= 0.397 Angle : 0.737 54.244 44046 Z= 0.435 Chirality : 0.049 0.422 5037 Planarity : 0.008 0.169 5610 Dihedral : 8.713 87.839 11668 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.69 % Allowed : 5.66 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.12), residues: 3993 helix: -0.29 (0.18), residues: 756 sheet: -0.86 (0.17), residues: 805 loop : -2.60 (0.11), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 66 TYR 0.014 0.001 TYR M 49 PHE 0.023 0.001 PHE B 185 TRP 0.009 0.001 TRP A 344 HIS 0.004 0.000 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.27 (32170) covalent geometry : angle 0.62850 / 0.40 (43846) SS BOND : bond 0.12816 / 8.52 ( 67) SS BOND : angle 6.68142 / 4.13 ( 134) hydrogen bonds : bond 0.17288 / 11.20 ( 1018) hydrogen bonds : angle 6.64199 / 4.53 ( 2868) link_NAG-ASN : bond 0.00472 / 0.27 ( 22) link_NAG-ASN : angle 2.99794 / 2.06 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 801 time to evaluate : 1.035 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: 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 51 VAL cc_start: 0.5370 (OUTLIER) cc_final: 0.4959 (t) REVERT: A 426 TYR cc_start: 0.5145 (m-80) cc_final: 0.4873 (m-80) REVERT: A 598 ASN cc_start: 0.5333 (m-40) cc_final: 0.4872 (t0) REVERT: A 787 GLU cc_start: 0.3415 (mt-10) cc_final: 0.3211 (mt-10) REVERT: A 950 LEU cc_start: 0.3718 (mt) cc_final: 0.3436 (mt) REVERT: A 1055 SER cc_start: 0.8439 (p) cc_final: 0.8077 (p) REVERT: A 1122 ASN cc_start: 0.6307 (m110) cc_final: 0.6014 (m110) REVERT: B 32 ILE cc_start: 0.4696 (OUTLIER) cc_final: 0.4172 (tt) REVERT: B 51 VAL cc_start: 0.0994 (OUTLIER) cc_final: 0.0281 (t) REVERT: B 606 ASP cc_start: 0.5595 (OUTLIER) cc_final: 0.5256 (p0) REVERT: B 609 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7055 (t80) REVERT: B 936 CYS cc_start: 0.4566 (m) cc_final: 0.4122 (p) REVERT: B 949 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.3458 (mt) REVERT: B 1043 LEU cc_start: 0.5917 (tp) cc_final: 0.5370 (tp) REVERT: B 1189 SER cc_start: 0.7257 (p) cc_final: 0.6740 (m) REVERT: C 909 ASN cc_start: 0.7575 (m-40) cc_final: 0.7201 (m-40) REVERT: C 1177 PHE cc_start: 0.5248 (m-80) cc_final: 0.3924 (m-10) outliers start: 95 outliers final: 21 residues processed: 863 average time/residue: 0.1900 time to fit residues: 266.5400 Evaluate side-chains 451 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 424 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 546 CYS Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 1148 TYR Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1176 TYR Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain M residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 142 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS A 433 ASN A 605 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 ASN A 709 GLN A 771 ASN A 789 GLN A 821 ASN A 847 ASN A1016 GLN A1023 ASN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 GLN ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 ASN A1128 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 243 ASN B 265 GLN B 372 ASN B 445 ASN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN B 587 ASN B 595 ASN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN B 630 GLN B 684 ASN B 722 ASN B 789 GLN B 821 ASN B 826 HIS B 872 ASN ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1023 ASN B1046 GLN B1049 ASN B1126 ASN B1206 ASN C 248 ASN C 465 HIS C 587 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 GLN C 826 HIS C 874 ASN C1006 ASN C1045 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.191423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.163430 restraints weight = 90608.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.163224 restraints weight = 59661.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.163272 restraints weight = 44428.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.163804 restraints weight = 42266.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.164025 restraints weight = 35989.148| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 32259 Z= 0.255 Angle : 0.890 31.603 44046 Z= 0.441 Chirality : 0.053 0.936 5037 Planarity : 0.006 0.152 5610 Dihedral : 6.613 101.793 4832 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer: Outliers : 4.25 % Allowed : 11.89 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.12), residues: 3993 helix: -0.15 (0.18), residues: 745 sheet: -0.78 (0.17), residues: 832 loop : -2.22 (0.11), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 693 TYR 0.029 0.003 TYR I 90 PHE 0.037 0.003 PHE C 774 TRP 0.039 0.003 TRP A 971 HIS 0.011 0.002 HIS B1129 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (32170) covalent geometry : angle 0.85729 / 0.43 (43846) SS BOND : bond 0.00459 / 0.31 ( 67) SS BOND : angle 1.90306 / 1.29 ( 134) hydrogen bonds : bond 0.04375 / 2.87 ( 1018) hydrogen bonds : angle 5.78353 / 3.93 ( 2868) link_NAG-ASN : bond 0.01546 / 1.21 ( 22) link_NAG-ASN : angle 5.72220 / 5.03 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 516 time to evaluate : 0.933 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: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.6387 (ttp) cc_final: 0.6168 (ttp) REVERT: A 598 ASN cc_start: 0.5115 (m-40) cc_final: 0.4820 (t0) REVERT: A 778 SER cc_start: 0.7119 (p) cc_final: 0.6797 (t) REVERT: A 870 ASN cc_start: 0.5983 (t0) cc_final: 0.5650 (t0) REVERT: A 1099 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 32 ILE cc_start: 0.4689 (OUTLIER) cc_final: 0.4146 (tt) REVERT: B 263 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7015 (ttm170) REVERT: B 291 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7310 (mm-40) REVERT: B 447 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6846 (ptp-170) REVERT: B 566 PHE cc_start: 0.6885 (t80) cc_final: 0.6658 (p90) REVERT: B 597 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.6840 (tp) REVERT: B 609 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7222 (t80) REVERT: B 672 CYS cc_start: 0.4018 (OUTLIER) cc_final: 0.3720 (m) REVERT: B 922 TYR cc_start: 0.6663 (m-10) cc_final: 0.6211 (m-80) REVERT: C 646 ASN cc_start: 0.6113 (p0) cc_final: 0.5374 (p0) REVERT: C 667 TYR cc_start: 0.4911 (m-80) cc_final: 0.4632 (m-80) REVERT: C 851 ASP cc_start: 0.7949 (m-30) cc_final: 0.7509 (m-30) REVERT: C 1204 PHE cc_start: 0.4272 (m-80) cc_final: 0.3913 (m-80) REVERT: I 72 ASP cc_start: 0.6139 (OUTLIER) cc_final: 0.5938 (m-30) REVERT: L 18 ARG cc_start: 0.6057 (ttp80) cc_final: 0.5551 (tpp80) REVERT: L 24 TRP cc_start: 0.6176 (m100) cc_final: 0.5713 (m100) REVERT: L 74 THR cc_start: 0.6862 (OUTLIER) cc_final: 0.6359 (p) REVERT: L 92 TYR cc_start: 0.5092 (t80) cc_final: 0.2628 (t80) outliers start: 150 outliers final: 62 residues processed: 624 average time/residue: 0.1795 time to fit residues: 187.6819 Evaluate side-chains 416 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 345 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 672 CYS Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 1083 THR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1148 TYR Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1121 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 51 optimal weight: 0.0970 chunk 265 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 258 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 171 optimal weight: 0.0970 chunk 335 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 HIS A 954 GLN A1016 GLN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 535 GLN ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 ASN B1023 ASN ** B1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 ASN ** B1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 ASN C 395 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 826 HIS C 909 ASN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.189725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.161934 restraints weight = 89626.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.159499 restraints weight = 64320.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.160763 restraints weight = 47294.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.161104 restraints weight = 36320.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.161266 restraints weight = 34752.965| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 32259 Z= 0.128 Angle : 0.601 11.560 44046 Z= 0.304 Chirality : 0.044 0.486 5037 Planarity : 0.004 0.082 5610 Dihedral : 5.062 59.858 4810 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 3.14 % Allowed : 15.40 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 3993 helix: 0.83 (0.19), residues: 749 sheet: -0.30 (0.18), residues: 830 loop : -2.02 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 320 TYR 0.026 0.002 TYR M 92 PHE 0.037 0.002 PHE B 968 TRP 0.022 0.002 TRP A 89 HIS 0.014 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (32170) covalent geometry : angle 0.58868 / 0.30 (43846) SS BOND : bond 0.00460 / 0.27 ( 67) SS BOND : angle 1.38504 / 1.03 ( 134) hydrogen bonds : bond 0.03391 / 2.24 ( 1018) hydrogen bonds : angle 5.02045 / 3.41 ( 2868) link_NAG-ASN : bond 0.00897 / 0.72 ( 22) link_NAG-ASN : angle 2.63786 / 2.10 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 373 time to evaluate : 0.964 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 744 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7826 (mt) REVERT: A 870 ASN cc_start: 0.6358 (t0) cc_final: 0.6038 (t0) REVERT: A 1099 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 1193 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.4814 (m-10) REVERT: B 32 ILE cc_start: 0.4342 (OUTLIER) cc_final: 0.3776 (tt) REVERT: B 210 TYR cc_start: 0.6690 (m-80) cc_final: 0.6135 (m-10) REVERT: B 447 ARG cc_start: 0.7101 (mtm180) cc_final: 0.6841 (ptp-170) REVERT: B 609 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7196 (t80) REVERT: B 619 CYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5433 (t) REVERT: B 746 TYR cc_start: 0.5904 (OUTLIER) cc_final: 0.4901 (m-80) REVERT: B 1094 SER cc_start: 0.8294 (m) cc_final: 0.7993 (m) REVERT: C 646 ASN cc_start: 0.6416 (p0) cc_final: 0.5930 (p0) REVERT: C 714 ASP cc_start: 0.7081 (t70) cc_final: 0.6769 (p0) REVERT: C 851 ASP cc_start: 0.8185 (m-30) cc_final: 0.7741 (m-30) REVERT: C 934 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7966 (mp) REVERT: I 92 CYS cc_start: 0.2141 (OUTLIER) cc_final: 0.1938 (p) REVERT: L 24 TRP cc_start: 0.5765 (m100) cc_final: 0.5381 (m100) REVERT: L 98 PHE cc_start: 0.4557 (m-80) cc_final: 0.3513 (m-80) REVERT: M 45 LYS cc_start: 0.4338 (tptt) cc_final: 0.4001 (tmmt) REVERT: M 46 LEU cc_start: 0.1195 (OUTLIER) cc_final: -0.0244 (tt) outliers start: 111 outliers final: 59 residues processed: 462 average time/residue: 0.1787 time to fit residues: 139.2043 Evaluate side-chains 381 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 312 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 744 ILE Chi-restraints excluded: chain A residue 799 HIS Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1167 ASP Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 936 CYS Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 350 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 288 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 228 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 826 HIS A 941 ASN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN A1201 ASN B 395 ASN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B 998 ASN ** B1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 847 ASN C1135 GLN C1201 ASN H 57 GLN H 102 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.179588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.147036 restraints weight = 84876.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.144113 restraints weight = 64768.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.145398 restraints weight = 48339.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.145989 restraints weight = 36214.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.146103 restraints weight = 33402.879| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 32259 Z= 0.193 Angle : 0.704 20.137 44046 Z= 0.358 Chirality : 0.047 0.571 5037 Planarity : 0.005 0.067 5610 Dihedral : 5.241 59.789 4804 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 4.53 % Allowed : 15.12 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.13), residues: 3993 helix: 0.75 (0.19), residues: 742 sheet: -0.37 (0.18), residues: 815 loop : -1.90 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 397 TYR 0.044 0.002 TYR C 622 PHE 0.055 0.002 PHE B 968 TRP 0.049 0.002 TRP B 344 HIS 0.008 0.001 HIS C 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (32170) covalent geometry : angle 0.69086 / 0.35 (43846) SS BOND : bond 0.01024 / 0.77 ( 67) SS BOND : angle 1.84795 / 1.44 ( 134) hydrogen bonds : bond 0.03996 / 2.60 ( 1018) hydrogen bonds : angle 5.17455 / 3.51 ( 2868) link_NAG-ASN : bond 0.00981 / 0.79 ( 22) link_NAG-ASN : angle 2.57228 / 2.03 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 405 time to evaluate : 1.235 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: A 147 GLU cc_start: 0.6449 (tp30) cc_final: 0.5944 (tt0) REVERT: A 163 CYS cc_start: 0.2576 (OUTLIER) cc_final: 0.2143 (t) REVERT: A 184 LEU cc_start: 0.7882 (mt) cc_final: 0.7672 (tp) REVERT: A 693 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7624 (ptm160) REVERT: A 711 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6605 (p90) REVERT: A 870 ASN cc_start: 0.6630 (t0) cc_final: 0.6274 (t0) REVERT: A 926 THR cc_start: 0.6990 (m) cc_final: 0.6660 (p) REVERT: A 995 ASP cc_start: 0.6462 (p0) cc_final: 0.6143 (t0) REVERT: A 1107 ILE cc_start: 0.8907 (mm) cc_final: 0.8492 (mt) REVERT: A 1139 TYR cc_start: 0.8144 (m-10) cc_final: 0.7790 (m-80) REVERT: A 1193 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5315 (m-10) REVERT: A 1196 PRO cc_start: 0.6320 (Cg_exo) cc_final: 0.5761 (Cg_endo) REVERT: A 1205 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.5532 (mpp) REVERT: B 135 TYR cc_start: 0.5091 (OUTLIER) cc_final: 0.2597 (m-80) REVERT: B 238 MET cc_start: 0.4583 (tpp) cc_final: 0.4275 (tpp) REVERT: B 263 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7729 (ttm170) REVERT: B 447 ARG cc_start: 0.7204 (mtm180) cc_final: 0.6859 (ptp-170) REVERT: B 609 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7238 (t80) REVERT: B 746 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5327 (m-80) REVERT: B 827 ASP cc_start: 0.6964 (m-30) cc_final: 0.6760 (m-30) REVERT: B 861 LEU cc_start: 0.9087 (mt) cc_final: 0.8850 (mt) REVERT: B 1008 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7907 (t80) REVERT: B 1034 ASN cc_start: 0.7553 (m-40) cc_final: 0.7218 (m-40) REVERT: B 1205 MET cc_start: 0.4924 (mmp) cc_final: 0.4145 (mtt) REVERT: C 117 LEU cc_start: 0.5214 (OUTLIER) cc_final: 0.4216 (pp) REVERT: C 238 MET cc_start: -0.0991 (mtm) cc_final: -0.1220 (mtt) REVERT: C 851 ASP cc_start: 0.8507 (m-30) cc_final: 0.8107 (m-30) REVERT: L 24 TRP cc_start: 0.5740 (m100) cc_final: 0.5128 (m100) REVERT: L 45 LYS cc_start: 0.6228 (mmmt) cc_final: 0.5716 (tptp) REVERT: L 98 PHE cc_start: 0.4251 (m-80) cc_final: 0.3549 (m-80) outliers start: 160 outliers final: 83 residues processed: 524 average time/residue: 0.1730 time to fit residues: 155.7882 Evaluate side-chains 424 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 330 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1167 ASP Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 731 VAL Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 936 CYS Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1201 ASN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 123 optimal weight: 8.9990 chunk 83 optimal weight: 0.0050 chunk 145 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN A 535 GLN A1036 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 GLN B 998 ASN B1016 GLN B1030 GLN C 243 ASN C 424 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 ASN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.174282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.141546 restraints weight = 82654.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.139763 restraints weight = 77563.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.140749 restraints weight = 57431.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.141287 restraints weight = 41281.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.141355 restraints weight = 36821.249| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 32259 Z= 0.199 Angle : 0.689 22.928 44046 Z= 0.351 Chirality : 0.047 0.493 5037 Planarity : 0.005 0.071 5610 Dihedral : 5.408 57.334 4802 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 3.85 % Allowed : 16.96 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3993 helix: 0.81 (0.19), residues: 747 sheet: -0.37 (0.18), residues: 819 loop : -1.85 (0.12), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 397 TYR 0.029 0.002 TYR B 692 PHE 0.037 0.002 PHE B 968 TRP 0.038 0.003 TRP M 24 HIS 0.014 0.002 HIS C 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (32170) covalent geometry : angle 0.66206 / 0.34 (43846) SS BOND : bond 0.00322 / 0.19 ( 67) SS BOND : angle 1.93250 / 1.56 ( 134) hydrogen bonds : bond 0.03628 / 2.36 ( 1018) hydrogen bonds : angle 5.04385 / 3.44 ( 2868) link_NAG-ASN : bond 0.01221 / 0.94 ( 22) link_NAG-ASN : angle 4.29632 / 3.60 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 373 time to evaluate : 1.100 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 147 GLU cc_start: 0.6746 (tp30) cc_final: 0.6264 (tt0) REVERT: A 151 CYS cc_start: 0.3987 (OUTLIER) cc_final: 0.3275 (m) REVERT: A 711 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6758 (p90) REVERT: A 851 ASP cc_start: 0.7464 (m-30) cc_final: 0.7181 (m-30) REVERT: A 870 ASN cc_start: 0.6864 (t0) cc_final: 0.6617 (t0) REVERT: A 926 THR cc_start: 0.7368 (m) cc_final: 0.7043 (p) REVERT: A 1107 ILE cc_start: 0.9006 (mm) cc_final: 0.8607 (mt) REVERT: A 1139 TYR cc_start: 0.8199 (m-10) cc_final: 0.7777 (m-80) REVERT: A 1193 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.5910 (m-80) REVERT: A 1205 MET cc_start: 0.6716 (tpp) cc_final: 0.6299 (mtt) REVERT: B 135 TYR cc_start: 0.4883 (OUTLIER) cc_final: 0.2337 (m-80) REVERT: B 151 CYS cc_start: 0.0987 (OUTLIER) cc_final: 0.0715 (m) REVERT: B 205 GLU cc_start: 0.7410 (tp30) cc_final: 0.6668 (tt0) REVERT: B 263 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7899 (ttt90) REVERT: B 271 ASP cc_start: 0.6233 (t0) cc_final: 0.6022 (t0) REVERT: B 447 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6823 (ptp-170) REVERT: B 609 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7280 (t80) REVERT: B 746 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.5723 (m-80) REVERT: B 1008 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 1034 ASN cc_start: 0.8163 (m-40) cc_final: 0.7935 (m-40) REVERT: B 1126 ASN cc_start: 0.7369 (p0) cc_final: 0.7079 (p0) REVERT: C 117 LEU cc_start: 0.4654 (OUTLIER) cc_final: 0.3591 (pp) REVERT: C 649 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.5470 (t80) REVERT: C 851 ASP cc_start: 0.8534 (m-30) cc_final: 0.8185 (m-30) REVERT: C 904 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7213 (mt-10) REVERT: C 934 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7934 (mp) REVERT: C 1205 MET cc_start: 0.4344 (mmp) cc_final: 0.2900 (mtp) REVERT: H 82 MET cc_start: 0.1470 (tmm) cc_final: 0.1245 (tmm) REVERT: L 45 LYS cc_start: 0.5685 (mmmt) cc_final: 0.5408 (tptp) REVERT: L 98 PHE cc_start: 0.4105 (m-80) cc_final: 0.3449 (m-80) outliers start: 136 outliers final: 78 residues processed: 474 average time/residue: 0.1630 time to fit residues: 133.4482 Evaluate side-chains 402 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 312 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1170 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1167 ASP Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1217 PHE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 649 TYR Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 936 CYS Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1157 LEU Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 5 optimal weight: 2.9990 chunk 195 optimal weight: 0.0770 chunk 118 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 318 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1016 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 353 ASN B 646 ASN B 702 ASN ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 GLN ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.174143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.140827 restraints weight = 82682.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.138381 restraints weight = 77042.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.139584 restraints weight = 53200.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.140318 restraints weight = 39079.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.140366 restraints weight = 35021.429| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.7966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32259 Z= 0.124 Angle : 0.602 18.047 44046 Z= 0.301 Chirality : 0.046 0.742 5037 Planarity : 0.004 0.057 5610 Dihedral : 5.071 57.500 4800 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 3.48 % Allowed : 18.20 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 3993 helix: 1.05 (0.20), residues: 751 sheet: -0.22 (0.18), residues: 836 loop : -1.81 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 900 TYR 0.020 0.001 TYR C 609 PHE 0.034 0.001 PHE B 968 TRP 0.038 0.002 TRP M 24 HIS 0.013 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (32170) covalent geometry : angle 0.58346 / 0.30 (43846) SS BOND : bond 0.00247 / 0.13 ( 67) SS BOND : angle 1.40371 / 1.11 ( 134) hydrogen bonds : bond 0.03267 / 2.14 ( 1018) hydrogen bonds : angle 4.87064 / 3.30 ( 2868) link_NAG-ASN : bond 0.00835 / 0.67 ( 22) link_NAG-ASN : angle 3.46927 / 2.97 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 350 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: A 693 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7985 (ptm160) REVERT: A 711 PHE cc_start: 0.7074 (OUTLIER) cc_final: 0.6744 (p90) REVERT: A 870 ASN cc_start: 0.6987 (t0) cc_final: 0.6724 (t0) REVERT: A 926 THR cc_start: 0.7296 (m) cc_final: 0.6932 (p) REVERT: A 1107 ILE cc_start: 0.9002 (mm) cc_final: 0.8549 (mp) REVERT: A 1193 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: B 135 TYR cc_start: 0.4876 (OUTLIER) cc_final: 0.2715 (m-80) REVERT: B 151 CYS cc_start: 0.1028 (OUTLIER) cc_final: 0.0549 (m) REVERT: B 185 PHE cc_start: 0.3881 (t80) cc_final: 0.3539 (t80) REVERT: B 205 GLU cc_start: 0.7481 (tp30) cc_final: 0.6801 (tt0) REVERT: B 263 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7934 (ttt90) REVERT: B 609 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7251 (t80) REVERT: B 619 CYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5701 (t) REVERT: B 746 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: B 1008 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8143 (t80) REVERT: B 1168 ARG cc_start: 0.6516 (mtm180) cc_final: 0.6293 (ttm110) REVERT: C 117 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.3787 (pp) REVERT: C 851 ASP cc_start: 0.8446 (m-30) cc_final: 0.8096 (m-30) REVERT: C 1008 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7601 (t80) REVERT: C 1180 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7896 (pp30) REVERT: C 1205 MET cc_start: 0.4262 (mmp) cc_final: 0.2918 (mtp) REVERT: H 82 MET cc_start: 0.1440 (tmm) cc_final: 0.1237 (tmm) REVERT: L 45 LYS cc_start: 0.5841 (mmmt) cc_final: 0.5504 (tptp) REVERT: L 98 PHE cc_start: 0.4248 (m-80) cc_final: 0.3287 (m-80) REVERT: M 11 LEU cc_start: 0.2807 (pp) cc_final: 0.2318 (tt) REVERT: M 24 TRP cc_start: 0.4155 (m100) cc_final: 0.3518 (m-90) outliers start: 123 outliers final: 83 residues processed: 437 average time/residue: 0.1750 time to fit residues: 131.3861 Evaluate side-chains 398 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 302 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1170 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 822 TYR Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 CYS Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1008 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1020 THR Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1180 GLN Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 365 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 195 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 234 HIS A 998 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 GLN A1201 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 GLN C 192 ASN C 445 ASN C 654 ASN C 847 ASN C 998 ASN C1135 GLN ** C1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.163021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.126899 restraints weight = 79489.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.121586 restraints weight = 78487.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.122923 restraints weight = 64183.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124040 restraints weight = 44355.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.124106 restraints weight = 39697.596| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.9638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 32259 Z= 0.323 Angle : 0.848 15.425 44046 Z= 0.437 Chirality : 0.052 0.510 5037 Planarity : 0.006 0.152 5610 Dihedral : 5.991 58.221 4800 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.54 % Favored : 92.39 % Rotamer: Outliers : 4.47 % Allowed : 17.98 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.13), residues: 3993 helix: 0.16 (0.19), residues: 749 sheet: -0.45 (0.18), residues: 835 loop : -1.89 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B 676 TYR 0.030 0.003 TYR B 625 PHE 0.055 0.003 PHE B 968 TRP 0.061 0.003 TRP A 971 HIS 0.036 0.003 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.32 (32170) covalent geometry : angle 0.83075 / 0.43 (43846) SS BOND : bond 0.00547 / 0.31 ( 67) SS BOND : angle 2.09677 / 1.63 ( 134) hydrogen bonds : bond 0.04679 / 3.03 ( 1018) hydrogen bonds : angle 5.66273 / 3.88 ( 2868) link_NAG-ASN : bond 0.00965 / 0.73 ( 22) link_NAG-ASN : angle 3.51649 / 2.76 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 324 time to evaluate : 1.226 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 79 LEU cc_start: 0.4947 (OUTLIER) cc_final: 0.4710 (tp) REVERT: A 89 TRP cc_start: 0.5209 (m-10) cc_final: 0.4986 (m-90) REVERT: A 151 CYS cc_start: 0.4156 (OUTLIER) cc_final: 0.3371 (m) REVERT: A 687 SER cc_start: 0.8496 (t) cc_final: 0.8128 (p) REVERT: A 711 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7377 (p90) REVERT: A 926 THR cc_start: 0.7656 (m) cc_final: 0.7088 (p) REVERT: A 1008 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8489 (t80) REVERT: A 1107 ILE cc_start: 0.9039 (mm) cc_final: 0.8646 (mt) REVERT: B 135 TYR cc_start: 0.5376 (OUTLIER) cc_final: 0.3555 (m-80) REVERT: B 185 PHE cc_start: 0.5174 (t80) cc_final: 0.4892 (t80) REVERT: B 238 MET cc_start: 0.4354 (tpp) cc_final: 0.3788 (tpp) REVERT: B 263 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8190 (ttt90) REVERT: B 609 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.7312 (t80) REVERT: B 676 ARG cc_start: 0.6727 (tpt170) cc_final: 0.6092 (tpp-160) REVERT: B 746 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: B 1008 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8309 (t80) REVERT: B 1059 GLN cc_start: 0.7999 (tp40) cc_final: 0.7794 (tp40) REVERT: B 1094 SER cc_start: 0.9297 (m) cc_final: 0.9093 (m) REVERT: B 1168 ARG cc_start: 0.6631 (mtm180) cc_final: 0.6244 (ttm110) REVERT: C 44 LEU cc_start: 0.8822 (mt) cc_final: 0.8621 (pt) REVERT: C 263 ARG cc_start: 0.4642 (mtp85) cc_final: 0.3615 (tmt-80) REVERT: C 851 ASP cc_start: 0.8577 (m-30) cc_final: 0.8202 (m-30) REVERT: C 967 MET cc_start: 0.8412 (mtp) cc_final: 0.8056 (mtp) REVERT: C 1008 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7531 (t80) outliers start: 158 outliers final: 101 residues processed: 444 average time/residue: 0.1753 time to fit residues: 131.8366 Evaluate side-chains 366 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 255 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1220 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 175 HIS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 915 ASP Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 813 ASP Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 936 CYS Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1008 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1074 ILE Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 24 PHE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 36 optimal weight: 20.0000 chunk 345 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 260 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 243 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 998 ASN ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN B1017 ASN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 GLN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.165655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.131691 restraints weight = 79652.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.129811 restraints weight = 65253.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.131212 restraints weight = 58114.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.131083 restraints weight = 37080.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.131914 restraints weight = 33544.122| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.9742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32259 Z= 0.141 Angle : 0.649 12.309 44046 Z= 0.328 Chirality : 0.046 0.516 5037 Planarity : 0.004 0.054 5610 Dihedral : 5.347 59.253 4797 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 3.00 % Allowed : 20.47 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 3993 helix: 0.69 (0.19), residues: 748 sheet: -0.30 (0.18), residues: 835 loop : -1.81 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1064 TYR 0.028 0.002 TYR B 673 PHE 0.045 0.002 PHE B 368 TRP 0.048 0.002 TRP M 24 HIS 0.012 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (32170) covalent geometry : angle 0.63218 / 0.32 (43846) SS BOND : bond 0.00302 / 0.15 ( 67) SS BOND : angle 1.62876 / 1.29 ( 134) hydrogen bonds : bond 0.03573 / 2.32 ( 1018) hydrogen bonds : angle 5.19651 / 3.54 ( 2868) link_NAG-ASN : bond 0.00676 / 0.56 ( 22) link_NAG-ASN : angle 3.19223 / 2.57 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 303 time to evaluate : 1.114 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 238 MET cc_start: 0.5832 (tpt) cc_final: 0.5122 (tpt) REVERT: A 687 SER cc_start: 0.8356 (t) cc_final: 0.8029 (p) REVERT: A 711 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6975 (p90) REVERT: A 926 THR cc_start: 0.7666 (m) cc_final: 0.7108 (p) REVERT: A 1139 TYR cc_start: 0.8336 (m-80) cc_final: 0.7443 (m-80) REVERT: B 135 TYR cc_start: 0.5255 (OUTLIER) cc_final: 0.3280 (m-80) REVERT: B 146 LEU cc_start: 0.4424 (mt) cc_final: 0.4208 (tp) REVERT: B 185 PHE cc_start: 0.4696 (t80) cc_final: 0.4354 (t80) REVERT: B 206 ARG cc_start: 0.7468 (mmp80) cc_final: 0.7041 (mmp-170) REVERT: B 238 MET cc_start: 0.4238 (tpp) cc_final: 0.3240 (tpp) REVERT: B 263 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8260 (ttt90) REVERT: B 344 TRP cc_start: 0.7795 (p-90) cc_final: 0.6783 (p-90) REVERT: B 609 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7158 (t80) REVERT: B 619 CYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5548 (t) REVERT: B 676 ARG cc_start: 0.6644 (tpt170) cc_final: 0.6065 (tpp-160) REVERT: B 746 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: B 822 TYR cc_start: 0.7858 (m-80) cc_final: 0.7538 (m-80) REVERT: B 848 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7436 (t0) REVERT: B 958 TYR cc_start: 0.8611 (m-10) cc_final: 0.7753 (m-80) REVERT: B 967 MET cc_start: 0.7156 (tmm) cc_final: 0.6022 (mtp) REVERT: B 1008 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8241 (t80) REVERT: C 646 ASN cc_start: 0.8139 (p0) cc_final: 0.7834 (p0) REVERT: C 851 ASP cc_start: 0.8525 (m-30) cc_final: 0.8181 (m-30) REVERT: C 967 MET cc_start: 0.8383 (mtp) cc_final: 0.7973 (mtp) REVERT: C 1008 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7438 (t80) REVERT: H 39 GLN cc_start: 0.4887 (tm-30) cc_final: 0.4627 (tm-30) REVERT: L 27 GLN cc_start: 0.6786 (mp10) cc_final: 0.6251 (mp10) REVERT: M 75 ILE cc_start: 0.0851 (pt) cc_final: 0.0549 (mp) outliers start: 106 outliers final: 75 residues processed: 384 average time/residue: 0.1621 time to fit residues: 105.8997 Evaluate side-chains 354 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 270 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 820 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 936 CYS Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1008 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 240 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 334 optimal weight: 0.5980 chunk 233 optimal weight: 0.6980 chunk 363 optimal weight: 9.9990 chunk 347 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 863 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.165619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.130294 restraints weight = 79800.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.126744 restraints weight = 60785.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.128528 restraints weight = 47786.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.128746 restraints weight = 33398.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.128917 restraints weight = 32255.584| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.9840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32259 Z= 0.137 Angle : 0.642 11.963 44046 Z= 0.323 Chirality : 0.045 0.500 5037 Planarity : 0.004 0.057 5610 Dihedral : 5.143 59.046 4795 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 2.52 % Allowed : 21.01 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 3993 helix: 0.81 (0.19), residues: 755 sheet: -0.33 (0.18), residues: 861 loop : -1.77 (0.12), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 206 TYR 0.023 0.002 TYR A 958 PHE 0.040 0.002 PHE A 884 TRP 0.044 0.002 TRP C 644 HIS 0.010 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (32170) covalent geometry : angle 0.62471 / 0.32 (43846) SS BOND : bond 0.00312 / 0.19 ( 67) SS BOND : angle 1.69987 / 1.28 ( 134) hydrogen bonds : bond 0.03446 / 2.26 ( 1018) hydrogen bonds : angle 5.06710 / 3.46 ( 2868) link_NAG-ASN : bond 0.00667 / 0.55 ( 22) link_NAG-ASN : angle 3.08412 / 2.49 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 290 time to evaluate : 1.086 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 151 CYS cc_start: 0.3704 (OUTLIER) cc_final: 0.2921 (m) REVERT: A 225 SER cc_start: 0.8734 (p) cc_final: 0.8511 (p) REVERT: A 238 MET cc_start: 0.5995 (tpt) cc_final: 0.5356 (tpt) REVERT: A 687 SER cc_start: 0.8324 (t) cc_final: 0.8065 (p) REVERT: A 711 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7025 (p90) REVERT: A 800 GLU cc_start: 0.7848 (pm20) cc_final: 0.7515 (pm20) REVERT: A 926 THR cc_start: 0.7725 (m) cc_final: 0.7204 (p) REVERT: A 1008 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8327 (t80) REVERT: A 1139 TYR cc_start: 0.8217 (m-80) cc_final: 0.7456 (m-80) REVERT: B 135 TYR cc_start: 0.5303 (OUTLIER) cc_final: 0.3500 (m-80) REVERT: B 146 LEU cc_start: 0.4657 (mt) cc_final: 0.4414 (tp) REVERT: B 185 PHE cc_start: 0.4784 (t80) cc_final: 0.4423 (t80) REVERT: B 238 MET cc_start: 0.4333 (tpp) cc_final: 0.3679 (tpp) REVERT: B 263 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8225 (ttt90) REVERT: B 344 TRP cc_start: 0.7767 (p-90) cc_final: 0.6966 (p-90) REVERT: B 609 TYR cc_start: 0.7926 (m-10) cc_final: 0.7166 (t80) REVERT: B 619 CYS cc_start: 0.5789 (OUTLIER) cc_final: 0.5478 (t) REVERT: B 746 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6184 (m-80) REVERT: B 958 TYR cc_start: 0.8519 (m-10) cc_final: 0.7520 (m-80) REVERT: B 967 MET cc_start: 0.6929 (tmm) cc_final: 0.6113 (mtp) REVERT: B 1008 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8133 (t80) REVERT: C 851 ASP cc_start: 0.8388 (m-30) cc_final: 0.8063 (m-30) REVERT: C 967 MET cc_start: 0.8207 (mtp) cc_final: 0.7811 (mtp) REVERT: C 1008 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7384 (t80) REVERT: H 39 GLN cc_start: 0.5003 (tm-30) cc_final: 0.4723 (tm-30) outliers start: 89 outliers final: 75 residues processed: 357 average time/residue: 0.1608 time to fit residues: 99.4664 Evaluate side-chains 354 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 270 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 894 GLN Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 936 CYS Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1008 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 321 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 210 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 chunk 350 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 319 optimal weight: 0.6980 chunk 18 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 821 ASN A 863 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 872 ASN B 894 GLN B1045 GLN ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 GLN C1180 GLN ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.166251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.130636 restraints weight = 79747.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.127303 restraints weight = 57211.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.128855 restraints weight = 52009.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.129001 restraints weight = 36654.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.129252 restraints weight = 31953.281| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.9911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32259 Z= 0.124 Angle : 0.632 12.741 44046 Z= 0.318 Chirality : 0.045 0.491 5037 Planarity : 0.004 0.055 5610 Dihedral : 5.008 58.934 4793 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 2.58 % Allowed : 21.21 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 3993 helix: 0.87 (0.19), residues: 763 sheet: -0.26 (0.18), residues: 864 loop : -1.69 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 206 TYR 0.023 0.001 TYR B1219 PHE 0.043 0.002 PHE A 884 TRP 0.050 0.002 TRP C 644 HIS 0.027 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (32170) covalent geometry : angle 0.61806 / 0.31 (43846) SS BOND : bond 0.00230 / 0.13 ( 67) SS BOND : angle 1.46427 / 1.11 ( 134) hydrogen bonds : bond 0.03371 / 2.21 ( 1018) hydrogen bonds : angle 4.96378 / 3.38 ( 2868) link_NAG-ASN : bond 0.00636 / 0.52 ( 22) link_NAG-ASN : angle 2.95777 / 2.41 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 292 time to evaluate : 1.039 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: A 151 CYS cc_start: 0.3711 (OUTLIER) cc_final: 0.2925 (m) REVERT: A 225 SER cc_start: 0.8642 (p) cc_final: 0.8421 (p) REVERT: A 238 MET cc_start: 0.6069 (tpt) cc_final: 0.5522 (tpt) REVERT: A 687 SER cc_start: 0.8422 (t) cc_final: 0.8145 (p) REVERT: A 711 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6990 (p90) REVERT: A 926 THR cc_start: 0.7699 (m) cc_final: 0.7150 (p) REVERT: A 1008 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8220 (t80) REVERT: B 135 TYR cc_start: 0.5284 (OUTLIER) cc_final: 0.3439 (m-80) REVERT: B 146 LEU cc_start: 0.4729 (mt) cc_final: 0.4527 (tp) REVERT: B 185 PHE cc_start: 0.4842 (t80) cc_final: 0.4427 (t80) REVERT: B 238 MET cc_start: 0.4320 (tpp) cc_final: 0.3664 (tpp) REVERT: B 263 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8219 (ttt90) REVERT: B 344 TRP cc_start: 0.7758 (p-90) cc_final: 0.6969 (p-90) REVERT: B 609 TYR cc_start: 0.7914 (m-10) cc_final: 0.7162 (t80) REVERT: B 746 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: B 872 ASN cc_start: 0.4349 (OUTLIER) cc_final: 0.4108 (t0) REVERT: B 958 TYR cc_start: 0.8511 (m-10) cc_final: 0.7898 (m-80) REVERT: B 967 MET cc_start: 0.6695 (tmm) cc_final: 0.6049 (mtp) REVERT: B 1008 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8145 (t80) REVERT: C 177 ASP cc_start: 0.1052 (OUTLIER) cc_final: 0.0566 (t70) REVERT: C 851 ASP cc_start: 0.8440 (m-30) cc_final: 0.8098 (m-30) REVERT: C 967 MET cc_start: 0.8221 (mtp) cc_final: 0.7833 (mtp) REVERT: C 1008 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7368 (t80) REVERT: C 1185 MET cc_start: 0.8005 (tpp) cc_final: 0.7793 (tmm) REVERT: M 24 TRP cc_start: 0.4468 (m100) cc_final: 0.3744 (m-90) outliers start: 91 outliers final: 71 residues processed: 359 average time/residue: 0.1515 time to fit residues: 94.1412 Evaluate side-chains 349 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 268 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1008 PHE Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 879 VAL Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 TYR Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 594 PHE Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 719 CYS Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 936 CYS Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 996 VAL Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1008 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 196 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.166078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.131075 restraints weight = 79941.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.127342 restraints weight = 61478.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.129451 restraints weight = 54495.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.129284 restraints weight = 36773.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.130064 restraints weight = 32726.919| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.9940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.513 32259 Z= 0.211 Angle : 0.807 58.931 44046 Z= 0.434 Chirality : 0.046 0.553 5037 Planarity : 0.004 0.070 5610 Dihedral : 5.016 59.355 4793 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.91 % Favored : 93.99 % Rotamer: Outliers : 2.58 % Allowed : 21.21 % Favored : 76.22 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.13), residues: 3993 helix: 0.87 (0.19), residues: 763 sheet: -0.26 (0.18), residues: 864 loop : -1.69 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 206 TYR 0.024 0.002 TYR B 958 PHE 0.109 0.002 PHE B 408 TRP 0.042 0.002 TRP C 644 HIS 0.021 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.21 (32170) covalent geometry : angle 0.78164 / 0.43 (43846) SS BOND : bond 0.00711 / 0.61 ( 67) SS BOND : angle 3.11635 / 2.53 ( 134) hydrogen bonds : bond 0.03376 / 2.21 ( 1018) hydrogen bonds : angle 4.96298 / 3.38 ( 2868) link_NAG-ASN : bond 0.00664 / 0.53 ( 22) link_NAG-ASN : angle 2.92981 / 2.40 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5754.46 seconds wall clock time: 100 minutes 20.58 seconds (6020.58 seconds total)