Starting phenix.real_space_refine on Thu Oct 29 12:42:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ygq_72938/10_2026/9ygq_72938.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ygq_72938/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ygq_72938/10_2026/9ygq_72938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ygq_72938/10_2026/9ygq_72938.map" model { file = "/net/cci-nas-00/data/ceres_data/9ygq_72938/10_2026/9ygq_72938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ygq_72938/10_2026/9ygq_72938.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/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: 7.23, per 1000 atoms: 0.23 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=69, 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 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 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: 2.92 Conformation dependent library (CDL) restraints added in 1.7 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: 1.46 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: 9.18 Time building geometry restraints manager: 3.99 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: 18679 17.57 - 35.14: 617 35.14 - 52.70: 114 52.70 - 70.27: 24 70.27 - 87.84: 3 Dihedral angle restraints: 19437 sinusoidal: 7657 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 19434 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: 2.22 - 2.75: 3077 2.75 - 3.29: 30749 3.29 - 3.83: 50998 3.83 - 4.36: 59218 4.36 - 4.90: 102635 Nonbonded interactions: 246677 Sorted by model distance: 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 nonbonded pdb=" OH TYR C1148 " pdb=" O SER C1190 " model vdw 2.281 3.040 nonbonded pdb=" OG SER B 122 " pdb=" O MET B 238 " model vdw 2.288 3.040 ... (remaining 246672 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: 10.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 34.860 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.580 ------------------------------------------------------------------------------- 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 32261 Z= 0.397 Angle : 0.737 54.244 44050 Z= 0.435 Chirality : 0.049 0.422 5037 Planarity : 0.008 0.169 5610 Dihedral : 8.713 87.839 11668 Min Nonbonded Distance : 2.217 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 0.12629 / 8.39 ( 69) SS BOND : angle 6.58694 / 4.07 ( 138) 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 : 1.159 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: 0.1893 time to fit residues: 265.9579 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 : 1.125 ------------------------------------------------------------------------------- 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: [197, 388, 215, 20, 132, 261, 248, 207, 155, 244, 183] 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 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 ** C 988 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1006 ASN C1045 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** H 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.192002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.163417 restraints weight = 90925.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.162531 restraints weight = 54197.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.163832 restraints weight = 46971.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.163895 restraints weight = 36470.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.164107 restraints weight = 34343.645| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 32261 Z= 0.252 Angle : 0.869 30.527 44050 Z= 0.430 Chirality : 0.053 0.929 5037 Planarity : 0.006 0.120 5610 Dihedral : 6.352 91.993 4832 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 4.08 % Allowed : 11.83 % Favored : 84.09 % 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: -2.09 (0.12), residues: 3993 helix: -0.02 (0.18), residues: 745 sheet: -0.69 (0.17), residues: 854 loop : -2.21 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 693 TYR 0.027 0.003 TYR I 90 PHE 0.036 0.003 PHE C 774 TRP 0.037 0.003 TRP A 971 HIS 0.012 0.002 HIS B1129 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.25 (32170) covalent geometry : angle 0.83643 / 0.42 (43846) SS BOND : bond 0.00704 / 0.45 ( 69) SS BOND : angle 1.88426 / 1.27 ( 138) hydrogen bonds : bond 0.04246 / 2.79 ( 1018) hydrogen bonds : angle 5.66372 / 3.85 ( 2868) link_NAG-ASN : bond 0.01391 / 1.02 ( 22) link_NAG-ASN : angle 5.64121 / 4.98 ( 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 659 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 515 time to evaluate : 1.164 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: A 218 MET cc_start: 0.6385 (ttp) cc_final: 0.6179 (ttp) REVERT: A 598 ASN cc_start: 0.5331 (m-40) cc_final: 0.5001 (t0) REVERT: A 778 SER cc_start: 0.6981 (p) cc_final: 0.6515 (t) REVERT: A 862 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5590 (mmm) REVERT: A 870 ASN cc_start: 0.5970 (t0) cc_final: 0.5679 (t0) REVERT: A 1099 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8706 (mp) REVERT: B 32 ILE cc_start: 0.4729 (OUTLIER) cc_final: 0.4211 (tt) REVERT: B 263 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6867 (ttm170) REVERT: B 291 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7206 (mm110) REVERT: B 408 PHE cc_start: 0.7006 (m-10) cc_final: 0.6765 (m-80) REVERT: B 447 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6818 (ptp-170) REVERT: B 566 PHE cc_start: 0.7031 (t80) cc_final: 0.6727 (p90) REVERT: B 609 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7219 (t80) REVERT: B 672 CYS cc_start: 0.4035 (OUTLIER) cc_final: 0.3762 (m) REVERT: B 1074 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8737 (mt) REVERT: C 646 ASN cc_start: 0.6276 (p0) cc_final: 0.5526 (p0) REVERT: C 851 ASP cc_start: 0.7921 (m-30) cc_final: 0.7513 (m-30) REVERT: C 1204 PHE cc_start: 0.4317 (m-80) cc_final: 0.3939 (m-80) REVERT: I 72 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.6027 (m-30) REVERT: I 77 GLN cc_start: 0.5743 (pt0) cc_final: 0.5501 (pm20) REVERT: L 2 ILE cc_start: 0.4995 (mt) cc_final: 0.4768 (mp) REVERT: L 18 ARG cc_start: 0.6199 (ttp80) cc_final: 0.5604 (tpp80) REVERT: L 74 THR cc_start: 0.7006 (OUTLIER) cc_final: 0.6516 (p) REVERT: M 45 LYS cc_start: 0.4809 (OUTLIER) cc_final: 0.4408 (tptt) outliers start: 144 outliers final: 63 residues processed: 617 average time/residue: 0.1707 time to fit residues: 177.4642 Evaluate side-chains 412 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 338 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 124 ILE 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 317 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 655 ILE 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 862 MET 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 336 VAL 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 555 LYS 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 1074 ILE 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 633 PHE 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 25 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 Chi-restraints excluded: chain M residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: [51, 265, 184, 258, 20, 133, 171, 335, 162, 11, 266] chunk 51 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 258 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 171 optimal weight: 20.0000 chunk 335 optimal weight: 0.3980 chunk 162 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 201 HIS A 954 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 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN ** B1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** B1030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 ASN B1126 ASN C 192 ASN C 395 ASN C 424 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 826 HIS ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 ASN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 HIS ** 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 = 0.4747 r_free = 0.4747 target = 0.185400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.157623 restraints weight = 87746.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.155752 restraints weight = 75023.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.157061 restraints weight = 54438.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.157585 restraints weight = 38203.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.157638 restraints weight = 35141.982| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32261 Z= 0.177 Angle : 0.640 10.131 44050 Z= 0.326 Chirality : 0.045 0.443 5037 Planarity : 0.004 0.080 5610 Dihedral : 5.133 58.276 4812 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 3.60 % Allowed : 15.12 % Favored : 81.29 % 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: -1.57 (0.13), residues: 3993 helix: 0.80 (0.19), residues: 743 sheet: -0.29 (0.18), residues: 823 loop : -2.02 (0.12), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 763 TYR 0.029 0.002 TYR M 92 PHE 0.040 0.002 PHE B 968 TRP 0.028 0.002 TRP A 89 HIS 0.014 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (32170) covalent geometry : angle 0.62807 / 0.32 (43846) SS BOND : bond 0.00797 / 0.36 ( 69) SS BOND : angle 1.37317 / 1.04 ( 138) hydrogen bonds : bond 0.03747 / 2.48 ( 1018) hydrogen bonds : angle 5.11706 / 3.49 ( 2868) link_NAG-ASN : bond 0.01262 / 0.91 ( 22) link_NAG-ASN : angle 2.74188 / 2.15 ( 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 521 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 394 time to evaluate : 1.138 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 147 GLU cc_start: 0.6172 (tp30) cc_final: 0.5690 (tt0) REVERT: A 266 TYR cc_start: 0.7823 (m-80) cc_final: 0.7392 (m-80) REVERT: A 711 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6559 (p90) REVERT: A 744 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7938 (mt) REVERT: A 870 ASN cc_start: 0.6261 (t0) cc_final: 0.5944 (t0) REVERT: A 940 PHE cc_start: 0.5342 (m-10) cc_final: 0.5089 (m-80) REVERT: A 995 ASP cc_start: 0.6282 (p0) cc_final: 0.6009 (t0) REVERT: A 1193 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.4967 (m-10) REVERT: B 32 ILE cc_start: 0.4201 (OUTLIER) cc_final: 0.3561 (tt) REVERT: B 291 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7315 (mm110) REVERT: B 447 ARG cc_start: 0.6938 (mtm180) cc_final: 0.6649 (ptp-170) REVERT: B 609 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7194 (t80) REVERT: B 673 TYR cc_start: 0.5754 (t80) cc_final: 0.5515 (t80) REVERT: B 746 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.5319 (m-80) REVERT: B 771 ASN cc_start: 0.4538 (OUTLIER) cc_final: 0.4329 (t0) REVERT: B 836 CYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6218 (t) REVERT: B 861 LEU cc_start: 0.8739 (mt) cc_final: 0.8379 (mt) REVERT: B 1008 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7586 (t80) REVERT: B 1094 SER cc_start: 0.8645 (m) cc_final: 0.8369 (m) REVERT: C 319 ARG cc_start: 0.5714 (ttt180) cc_final: 0.5204 (mtp180) REVERT: C 851 ASP cc_start: 0.8468 (m-30) cc_final: 0.7973 (m-30) REVERT: C 1154 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7712 (ptmm) REVERT: L 98 PHE cc_start: 0.4246 (m-80) cc_final: 0.3709 (m-80) REVERT: M 46 LEU cc_start: 0.0807 (OUTLIER) cc_final: 0.0601 (tt) outliers start: 127 outliers final: 61 residues processed: 496 average time/residue: 0.1685 time to fit residues: 142.2528 Evaluate side-chains 393 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 321 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 GLU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 744 ILE 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 977 VAL 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 1104 SER 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 197 TRP 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 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 728 SER Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 771 ASN Chi-restraints excluded: chain B residue 836 CYS Chi-restraints excluded: chain B residue 972 SER 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 1151 THR 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 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 633 PHE 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 936 CYS Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 59 TYR 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: [350, 133, 229, 50, 33, 196, 149, 288, 150, 228, 180] chunk 350 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 288 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 228 optimal weight: 0.5980 chunk 180 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 ASN A 826 HIS ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 ASN B 621 ASN ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN ** B1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.182879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.154385 restraints weight = 86080.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.152753 restraints weight = 71312.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.153933 restraints weight = 55828.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.154756 restraints weight = 37617.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.154763 restraints weight = 33679.426| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 32261 Z= 0.138 Angle : 0.598 15.287 44050 Z= 0.304 Chirality : 0.044 0.515 5037 Planarity : 0.004 0.082 5610 Dihedral : 5.020 59.920 4806 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 3.82 % Allowed : 15.80 % Favored : 80.38 % 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: -1.40 (0.13), residues: 3993 helix: 0.98 (0.19), residues: 756 sheet: -0.19 (0.18), residues: 794 loop : -1.92 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 396 TYR 0.021 0.001 TYR L 36 PHE 0.043 0.002 PHE B 968 TRP 0.029 0.002 TRP B 344 HIS 0.013 0.001 HIS H 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (32170) covalent geometry : angle 0.58343 / 0.30 (43846) SS BOND : bond 0.00921 / 0.33 ( 69) SS BOND : angle 1.70067 / 1.33 ( 138) hydrogen bonds : bond 0.03240 / 2.12 ( 1018) hydrogen bonds : angle 4.93185 / 3.35 ( 2868) link_NAG-ASN : bond 0.00763 / 0.64 ( 22) link_NAG-ASN : angle 2.47647 / 1.98 ( 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 515 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 380 time to evaluate : 1.063 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 266 TYR cc_start: 0.7909 (m-80) cc_final: 0.7663 (m-80) REVERT: A 693 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7187 (ptm160) REVERT: A 711 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6449 (p90) REVERT: A 870 ASN cc_start: 0.6643 (t0) cc_final: 0.6287 (t0) REVERT: A 926 THR cc_start: 0.6645 (m) cc_final: 0.6376 (p) REVERT: A 1107 ILE cc_start: 0.8856 (mm) cc_final: 0.8472 (mt) REVERT: A 1193 TYR cc_start: 0.5769 (OUTLIER) cc_final: 0.5019 (m-10) REVERT: A 1205 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5468 (mpp) REVERT: B 263 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7609 (ttm170) REVERT: B 291 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7364 (mm110) REVERT: B 447 ARG cc_start: 0.6966 (mtm180) cc_final: 0.6602 (ptp-170) REVERT: B 609 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7178 (t80) REVERT: B 746 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5057 (m-80) REVERT: B 1008 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7608 (t80) REVERT: B 1034 ASN cc_start: 0.7292 (m-40) cc_final: 0.6984 (m-40) REVERT: B 1094 SER cc_start: 0.8658 (m) cc_final: 0.8442 (m) REVERT: C 117 LEU cc_start: 0.4577 (OUTLIER) cc_final: 0.3629 (pp) REVERT: C 319 ARG cc_start: 0.6143 (ttt180) cc_final: 0.5341 (mtp180) REVERT: C 851 ASP cc_start: 0.8453 (m-30) cc_final: 0.7948 (m-30) REVERT: H 82 MET cc_start: 0.2799 (tmm) cc_final: 0.2566 (tmm) REVERT: L 27 GLN cc_start: 0.6876 (mp10) cc_final: 0.6355 (mp10) REVERT: L 98 PHE cc_start: 0.4284 (m-80) cc_final: 0.3673 (m-80) REVERT: M 46 LEU cc_start: 0.0530 (OUTLIER) cc_final: 0.0292 (tt) outliers start: 135 outliers final: 71 residues processed: 480 average time/residue: 0.1719 time to fit residues: 141.4125 Evaluate side-chains 412 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 331 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE 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 205 GLU 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 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 1077 LEU Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1170 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1205 MET Chi-restraints excluded: chain A residue 1218 ILE 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 237 VAL Chi-restraints excluded: chain B residue 263 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 371 ASN 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 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 1008 PHE Chi-restraints excluded: chain B residue 1085 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 57 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 287 LEU 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 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 826 HIS Chi-restraints excluded: chain C residue 828 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 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 1154 LYS 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 I residue 59 TYR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: [123, 83, 145, 166, 173, 139, 131, 85, 42, 186, 76] chunk 123 optimal weight: 7.9990 chunk 83 optimal weight: 0.0970 chunk 145 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 76 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 872 ASN ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 GLN H 57 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.182033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.151593 restraints weight = 86506.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.150758 restraints weight = 70945.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.151761 restraints weight = 47682.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.152443 restraints weight = 36687.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.152486 restraints weight = 32233.406| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 32261 Z= 0.118 Angle : 0.586 13.557 44050 Z= 0.293 Chirality : 0.044 0.543 5037 Planarity : 0.004 0.064 5610 Dihedral : 5.109 57.968 4804 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 3.37 % Allowed : 16.28 % 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: -1.24 (0.13), residues: 3993 helix: 1.24 (0.20), residues: 747 sheet: -0.06 (0.19), residues: 771 loop : -1.84 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 397 TYR 0.022 0.001 TYR C 985 PHE 0.042 0.001 PHE B 968 TRP 0.018 0.001 TRP A 89 HIS 0.005 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (32170) covalent geometry : angle 0.57139 / 0.29 (43846) SS BOND : bond 0.00191 / 0.11 ( 69) SS BOND : angle 1.47375 / 1.21 ( 138) hydrogen bonds : bond 0.03172 / 2.07 ( 1018) hydrogen bonds : angle 4.79393 / 3.26 ( 2868) link_NAG-ASN : bond 0.00872 / 0.71 ( 22) link_NAG-ASN : angle 2.81543 / 2.38 ( 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 475 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 356 time to evaluate : 1.222 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 238 MET cc_start: 0.6125 (ttm) cc_final: 0.5649 (ttt) REVERT: A 711 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6401 (p90) REVERT: A 744 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8152 (mt) REVERT: A 870 ASN cc_start: 0.6670 (t0) cc_final: 0.6316 (t0) REVERT: A 926 THR cc_start: 0.6818 (m) cc_final: 0.6506 (p) REVERT: A 1107 ILE cc_start: 0.8878 (mm) cc_final: 0.8499 (mt) REVERT: A 1193 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.4963 (m-10) REVERT: B 238 MET cc_start: 0.4399 (tpp) cc_final: 0.3824 (tpp) REVERT: B 263 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7676 (ttm170) REVERT: B 447 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6589 (ptp-170) REVERT: B 609 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7193 (t80) REVERT: B 619 CYS cc_start: 0.6067 (OUTLIER) cc_final: 0.5596 (t) REVERT: B 746 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.5207 (m-80) REVERT: B 836 CYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6230 (t) REVERT: B 867 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8361 (mp) REVERT: B 1008 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7785 (t80) REVERT: B 1034 ASN cc_start: 0.7535 (m-40) cc_final: 0.7141 (m-40) REVERT: B 1094 SER cc_start: 0.8686 (m) cc_final: 0.8411 (m) REVERT: C 57 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7408 (pt) REVERT: C 117 LEU cc_start: 0.4687 (OUTLIER) cc_final: 0.3705 (pp) REVERT: C 319 ARG cc_start: 0.6150 (ttt180) cc_final: 0.5428 (mtp180) REVERT: C 649 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.5404 (t80) REVERT: C 851 ASP cc_start: 0.8424 (m-30) cc_final: 0.7987 (m-30) REVERT: H 82 MET cc_start: 0.2478 (tmm) cc_final: 0.2271 (tmm) REVERT: L 27 GLN cc_start: 0.6906 (mp10) cc_final: 0.6652 (mp10) REVERT: L 98 PHE cc_start: 0.4241 (m-80) cc_final: 0.3352 (m-80) REVERT: M 45 LYS cc_start: 0.2922 (pptt) cc_final: 0.1836 (tppt) outliers start: 119 outliers final: 70 residues processed: 451 average time/residue: 0.1654 time to fit residues: 129.0190 Evaluate side-chains 398 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 315 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 221 THR Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 744 ILE 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 1077 LEU Chi-restraints excluded: chain A residue 1096 ILE 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 237 VAL 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 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 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 836 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1096 ILE 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 57 LEU 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 176 ILE Chi-restraints excluded: chain C residue 287 LEU 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 633 PHE Chi-restraints excluded: chain C residue 649 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 744 ILE Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 826 HIS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER 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 1013 LEU Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1187 THR Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: [5, 195, 118, 87, 48, 270, 261, 318, 90, 7, 154] chunk 5 optimal weight: 3.9990 chunk 195 optimal weight: 0.0970 chunk 118 optimal weight: 0.0870 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 270 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 318 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 702 ASN B 872 ASN ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 ASN B1045 GLN ** B1092 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 ASN C 351 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.180829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.149137 restraints weight = 85411.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.147115 restraints weight = 61340.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.148300 restraints weight = 44274.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.148711 restraints weight = 33516.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.148808 restraints weight = 31920.541| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32261 Z= 0.115 Angle : 0.581 14.845 44050 Z= 0.293 Chirality : 0.044 0.554 5037 Planarity : 0.004 0.061 5610 Dihedral : 4.853 57.306 4804 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 3.45 % Allowed : 17.21 % Favored : 79.33 % 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: -1.09 (0.13), residues: 3993 helix: 1.39 (0.20), residues: 755 sheet: 0.02 (0.18), residues: 799 loop : -1.78 (0.12), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 676 TYR 0.034 0.001 TYR C 985 PHE 0.021 0.001 PHE A 884 TRP 0.019 0.001 TRP M 24 HIS 0.008 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (32170) covalent geometry : angle 0.56643 / 0.29 (43846) SS BOND : bond 0.00171 / 0.10 ( 69) SS BOND : angle 1.61560 / 1.20 ( 138) hydrogen bonds : bond 0.03131 / 2.04 ( 1018) hydrogen bonds : angle 4.68742 / 3.18 ( 2868) link_NAG-ASN : bond 0.00999 / 0.79 ( 22) link_NAG-ASN : angle 2.65794 / 2.19 ( 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 476 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 354 time to evaluate : 1.124 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 238 MET cc_start: 0.5980 (ttm) cc_final: 0.5528 (ttt) REVERT: A 693 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7312 (ptm160) REVERT: A 711 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.6395 (p90) REVERT: A 744 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8016 (mm) REVERT: A 788 ILE cc_start: 0.6109 (mm) cc_final: 0.5826 (mt) REVERT: A 870 ASN cc_start: 0.6585 (t0) cc_final: 0.6277 (t0) REVERT: A 926 THR cc_start: 0.6643 (m) cc_final: 0.6376 (p) REVERT: A 958 TYR cc_start: 0.7827 (m-10) cc_final: 0.7579 (m-10) REVERT: A 1107 ILE cc_start: 0.8942 (mm) cc_final: 0.8539 (mt) REVERT: A 1193 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.5080 (m-10) REVERT: A 1205 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5261 (mpp) REVERT: B 135 TYR cc_start: 0.5063 (OUTLIER) cc_final: 0.2882 (m-80) REVERT: B 238 MET cc_start: 0.4259 (tpp) cc_final: 0.3055 (tpp) REVERT: B 263 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7800 (ttt90) REVERT: B 344 TRP cc_start: 0.7693 (p-90) cc_final: 0.7180 (p-90) REVERT: B 609 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7233 (t80) REVERT: B 619 CYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5446 (t) REVERT: B 746 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.5219 (m-80) REVERT: B 839 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8923 (mt) REVERT: B 1008 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7964 (t80) REVERT: B 1034 ASN cc_start: 0.7688 (m-40) cc_final: 0.7410 (m-40) REVERT: B 1094 SER cc_start: 0.8716 (m) cc_final: 0.8455 (m) REVERT: B 1205 MET cc_start: 0.5601 (mmp) cc_final: 0.4681 (mtt) REVERT: C 57 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7515 (pt) REVERT: C 117 LEU cc_start: 0.5012 (OUTLIER) cc_final: 0.4000 (pp) REVERT: C 649 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5461 (t80) REVERT: C 851 ASP cc_start: 0.8497 (m-30) cc_final: 0.8079 (m-30) REVERT: H 82 MET cc_start: 0.2325 (tmm) cc_final: 0.1882 (tmm) REVERT: M 45 LYS cc_start: 0.3096 (pptt) cc_final: 0.2236 (tppt) outliers start: 122 outliers final: 77 residues processed: 445 average time/residue: 0.1656 time to fit residues: 126.8430 Evaluate side-chains 415 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 323 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG 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 221 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 744 ILE 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 861 LEU 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 1162 LEU Chi-restraints excluded: chain A residue 1170 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1205 MET 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 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 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 728 SER 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 807 SER Chi-restraints excluded: chain B residue 813 ASP Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 848 ASP Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1096 ILE 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 57 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 176 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 633 PHE Chi-restraints excluded: chain C residue 649 TYR Chi-restraints excluded: chain C residue 655 ILE 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 826 HIS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 865 VAL 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 1013 LEU Chi-restraints excluded: chain C residue 1126 ASN Chi-restraints excluded: chain C residue 1132 SER Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1170 ILE 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 L residue 2 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: [365, 158, 386, 213, 262, 206, 195, 114, 357, 229, 201] chunk 365 optimal weight: 20.0000 chunk 158 optimal weight: 0.1980 chunk 386 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 chunk 195 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 941 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 GLN C 445 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 ASN ** C 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 GLN C1201 ASN ** 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 = 0.4599 r_free = 0.4599 target = 0.172455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.138208 restraints weight = 82152.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.135295 restraints weight = 75058.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.136210 restraints weight = 55619.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.136852 restraints weight = 41782.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.137011 restraints weight = 36495.403| |-----------------------------------------------------------------------------| r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.8093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32261 Z= 0.191 Angle : 0.670 14.277 44050 Z= 0.341 Chirality : 0.046 0.514 5037 Planarity : 0.005 0.098 5610 Dihedral : 5.159 56.489 4802 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 3.94 % Allowed : 17.02 % Favored : 79.05 % 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: -1.20 (0.13), residues: 3993 helix: 1.11 (0.19), residues: 751 sheet: -0.14 (0.18), residues: 826 loop : -1.76 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 676 TYR 0.044 0.002 TYR M 49 PHE 0.045 0.002 PHE L 98 TRP 0.029 0.002 TRP L 24 HIS 0.007 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (32170) covalent geometry : angle 0.65658 / 0.34 (43846) SS BOND : bond 0.00339 / 0.17 ( 69) SS BOND : angle 1.69282 / 1.34 ( 138) hydrogen bonds : bond 0.03610 / 2.36 ( 1018) hydrogen bonds : angle 4.99543 / 3.42 ( 2868) link_NAG-ASN : bond 0.00796 / 0.63 ( 22) link_NAG-ASN : angle 2.70647 / 2.23 ( 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 498 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 359 time to evaluate : 1.204 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: 0.8454 (OUTLIER) cc_final: 0.8223 (ptp-170) REVERT: A 711 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6759 (p90) REVERT: A 851 ASP cc_start: 0.7442 (m-30) cc_final: 0.7142 (m-30) REVERT: A 870 ASN cc_start: 0.6990 (t0) cc_final: 0.6769 (t0) REVERT: A 926 THR cc_start: 0.7460 (m) cc_final: 0.7008 (p) REVERT: A 994 MET cc_start: 0.8230 (mmm) cc_final: 0.7870 (mmm) REVERT: A 1008 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8310 (t80) REVERT: A 1107 ILE cc_start: 0.9032 (mm) cc_final: 0.8628 (mt) REVERT: A 1139 TYR cc_start: 0.8190 (m-10) cc_final: 0.7834 (m-80) REVERT: A 1205 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6702 (mtt) REVERT: B 135 TYR cc_start: 0.5159 (OUTLIER) cc_final: 0.3210 (m-80) REVERT: B 226 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.5672 (tt) REVERT: B 238 MET cc_start: 0.4725 (tpp) cc_final: 0.4232 (tpp) REVERT: B 263 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8080 (ttt90) REVERT: B 462 TYR cc_start: 0.6143 (p90) cc_final: 0.5922 (p90) REVERT: B 609 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7265 (t80) REVERT: B 721 LEU cc_start: 0.7826 (mt) cc_final: 0.7186 (tt) REVERT: B 746 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.5752 (m-80) REVERT: B 839 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9067 (mt) REVERT: B 967 MET cc_start: 0.6629 (tmm) cc_final: 0.5482 (mmm) REVERT: B 990 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7874 (tp) REVERT: B 1008 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8225 (t80) REVERT: B 1126 ASN cc_start: 0.7430 (p0) cc_final: 0.7107 (p0) REVERT: C 203 TYR cc_start: 0.3190 (OUTLIER) cc_final: 0.1895 (p90) REVERT: C 851 ASP cc_start: 0.8555 (m-30) cc_final: 0.8119 (m-30) REVERT: C 1010 LYS cc_start: 0.8342 (tptp) cc_final: 0.8013 (ttpt) REVERT: C 1205 MET cc_start: 0.4162 (mmp) cc_final: 0.2999 (mtp) REVERT: L 24 TRP cc_start: 0.4633 (m100) cc_final: 0.4318 (m100) REVERT: M 45 LYS cc_start: 0.3405 (pptt) cc_final: 0.2735 (tppt) REVERT: M 46 LEU cc_start: 0.1405 (OUTLIER) cc_final: 0.0550 (tp) REVERT: M 70 ASP cc_start: 0.6319 (t0) cc_final: 0.6101 (t0) outliers start: 139 outliers final: 89 residues processed: 464 average time/residue: 0.1724 time to fit residues: 136.2254 Evaluate side-chains 410 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 307 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG 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 649 TYR Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 711 PHE Chi-restraints excluded: chain A residue 746 TYR 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 861 LEU 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 1008 PHE Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1170 ILE 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 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 197 TRP Chi-restraints excluded: chain B residue 226 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 371 ASN Chi-restraints excluded: chain B residue 374 ASP 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 728 SER 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 807 SER 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 862 MET Chi-restraints excluded: chain B residue 872 ASN 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 1054 ILE Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1162 LEU 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 61 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 203 TYR Chi-restraints excluded: chain C residue 240 LEU 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 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 777 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 907 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 1013 LEU Chi-restraints excluded: chain C residue 1126 ASN 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 31 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: [36, 345, 191, 260, 62, 243, 115, 110, 102, 67, 255] chunk 36 optimal weight: 20.0000 chunk 345 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 ASN A1030 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 646 ASN B 872 ASN B 894 GLN B 938 GLN C 323 ASN C 445 ASN C 645 GLN C1180 GLN C1201 ASN ** 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 = 0.4596 r_free = 0.4596 target = 0.172389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.138424 restraints weight = 81945.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.136083 restraints weight = 71852.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.137166 restraints weight = 50025.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.137686 restraints weight = 37293.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.137823 restraints weight = 33462.776| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.8415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 32261 Z= 0.133 Angle : 0.618 12.421 44050 Z= 0.309 Chirality : 0.044 0.503 5037 Planarity : 0.004 0.052 5610 Dihedral : 5.854 119.732 4800 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.14 % Rotamer: Outliers : 3.34 % Allowed : 18.26 % Favored : 78.40 % 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: -1.08 (0.13), residues: 3993 helix: 1.27 (0.20), residues: 755 sheet: -0.04 (0.18), residues: 808 loop : -1.71 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 676 TYR 0.030 0.001 TYR L 86 PHE 0.032 0.002 PHE B 968 TRP 0.025 0.002 TRP M 24 HIS 0.005 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (32170) covalent geometry : angle 0.60338 / 0.31 (43846) SS BOND : bond 0.00260 / 0.16 ( 69) SS BOND : angle 1.52903 / 1.09 ( 138) hydrogen bonds : bond 0.03275 / 2.12 ( 1018) hydrogen bonds : angle 4.86638 / 3.33 ( 2868) link_NAG-ASN : bond 0.00708 / 0.58 ( 22) link_NAG-ASN : angle 2.80633 / 2.18 ( 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 454 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 336 time to evaluate : 1.185 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: A 693 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8070 (ptm160) REVERT: A 711 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6663 (p90) REVERT: A 736 LEU cc_start: 0.7768 (mt) cc_final: 0.7514 (mp) REVERT: A 851 ASP cc_start: 0.7410 (m-30) cc_final: 0.7204 (m-30) REVERT: A 870 ASN cc_start: 0.7046 (t0) cc_final: 0.6819 (t0) REVERT: A 926 THR cc_start: 0.7403 (m) cc_final: 0.6852 (p) REVERT: A 994 MET cc_start: 0.8100 (mmm) cc_final: 0.7747 (mmm) REVERT: A 1107 ILE cc_start: 0.8886 (mm) cc_final: 0.8441 (mp) REVERT: B 135 TYR cc_start: 0.4783 (OUTLIER) cc_final: 0.3053 (m-80) REVERT: B 185 PHE cc_start: 0.4454 (t80) cc_final: 0.4241 (t80) REVERT: B 238 MET cc_start: 0.4712 (tpp) cc_final: 0.4029 (tpp) REVERT: B 263 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8072 (ttt90) REVERT: B 287 LEU cc_start: 0.7295 (mp) cc_final: 0.7058 (pp) REVERT: B 344 TRP cc_start: 0.7859 (p-90) cc_final: 0.7039 (p-90) REVERT: B 609 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7179 (t80) REVERT: B 696 LYS cc_start: 0.6968 (mmtm) cc_final: 0.6741 (mmtm) REVERT: B 721 LEU cc_start: 0.7840 (mt) cc_final: 0.7055 (tp) REVERT: B 746 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.5579 (m-80) REVERT: B 839 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8940 (mt) REVERT: B 967 MET cc_start: 0.6266 (tmm) cc_final: 0.5465 (mmm) REVERT: B 1008 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8296 (t80) REVERT: B 1126 ASN cc_start: 0.7356 (p0) cc_final: 0.6965 (p0) REVERT: C 609 TYR cc_start: 0.5571 (m-80) cc_final: 0.5360 (m-10) REVERT: C 851 ASP cc_start: 0.8522 (m-30) cc_final: 0.8139 (m-30) REVERT: C 1008 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7605 (t80) REVERT: C 1205 MET cc_start: 0.4265 (mmp) cc_final: 0.3348 (mtp) REVERT: M 45 LYS cc_start: 0.3058 (pptt) cc_final: 0.2448 (tppt) outliers start: 118 outliers final: 82 residues processed: 422 average time/residue: 0.1709 time to fit residues: 123.4626 Evaluate side-chains 401 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 310 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 670 LEU 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 861 LEU 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 1162 LEU Chi-restraints excluded: chain A residue 1170 ILE 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 57 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 175 HIS 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 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 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 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1204 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 61 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 176 ILE 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 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 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 936 CYS 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 1132 SER Chi-restraints excluded: chain C residue 1154 LYS Chi-restraints excluded: chain C residue 1170 ILE Chi-restraints excluded: chain C residue 1180 GLN Chi-restraints excluded: chain C residue 1201 ASN Chi-restraints excluded: chain I residue 31 THR 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 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: [240, 114, 272, 277, 135, 87, 39, 334, 233, 363, 347] chunk 240 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 277 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 chunk 334 optimal weight: 0.9990 chunk 233 optimal weight: 0.5980 chunk 363 optimal weight: 3.9990 chunk 347 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 872 ASN C 323 ASN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 GLN C1201 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.171292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.136116 restraints weight = 81554.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.133527 restraints weight = 59263.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.135353 restraints weight = 48747.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.135060 restraints weight = 36489.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.135308 restraints weight = 31720.894| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.8661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32261 Z= 0.135 Angle : 0.630 20.184 44050 Z= 0.315 Chirality : 0.044 0.486 5037 Planarity : 0.004 0.056 5610 Dihedral : 5.801 114.034 4800 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 2.92 % Allowed : 19.14 % Favored : 77.94 % 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: -1.05 (0.13), residues: 3993 helix: 1.27 (0.20), residues: 762 sheet: -0.12 (0.18), residues: 842 loop : -1.66 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1064 TYR 0.034 0.001 TYR B 625 PHE 0.036 0.002 PHE A 884 TRP 0.065 0.002 TRP M 24 HIS 0.008 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (32170) covalent geometry : angle 0.61936 / 0.31 (43846) SS BOND : bond 0.00230 / 0.13 ( 69) SS BOND : angle 1.41120 / 1.04 ( 138) hydrogen bonds : bond 0.03312 / 2.16 ( 1018) hydrogen bonds : angle 4.86700 / 3.32 ( 2868) link_NAG-ASN : bond 0.00586 / 0.48 ( 22) link_NAG-ASN : angle 2.43906 / 1.91 ( 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 417 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 314 time to evaluate : 1.208 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 687 SER cc_start: 0.8258 (t) cc_final: 0.7800 (p) REVERT: A 693 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8020 (ptm160) REVERT: A 711 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6687 (p90) REVERT: A 736 LEU cc_start: 0.7841 (mt) cc_final: 0.7588 (mp) REVERT: A 870 ASN cc_start: 0.7223 (t0) cc_final: 0.7003 (t0) REVERT: A 926 THR cc_start: 0.7522 (m) cc_final: 0.7024 (p) REVERT: A 994 MET cc_start: 0.8150 (mmm) cc_final: 0.7824 (mmm) REVERT: A 1107 ILE cc_start: 0.8856 (mm) cc_final: 0.8408 (mp) REVERT: B 135 TYR cc_start: 0.4864 (OUTLIER) cc_final: 0.3096 (m-80) REVERT: B 238 MET cc_start: 0.4691 (tpp) cc_final: 0.3944 (tpp) REVERT: B 263 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8188 (ttt90) REVERT: B 344 TRP cc_start: 0.7927 (p-90) cc_final: 0.7200 (p-90) REVERT: B 609 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7199 (t80) REVERT: B 746 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.5481 (m-80) REVERT: B 839 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8958 (mt) REVERT: B 967 MET cc_start: 0.6198 (tmm) cc_final: 0.5661 (mmm) REVERT: B 1008 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8237 (t80) REVERT: C 851 ASP cc_start: 0.8583 (m-30) cc_final: 0.8215 (m-30) REVERT: C 1008 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.7517 (t80) REVERT: C 1180 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8070 (pp30) REVERT: C 1205 MET cc_start: 0.4422 (mmp) cc_final: 0.3501 (mtp) REVERT: M 45 LYS cc_start: 0.3299 (pptt) cc_final: 0.2651 (tppt) outliers start: 103 outliers final: 84 residues processed: 387 average time/residue: 0.1635 time to fit residues: 109.5471 Evaluate side-chains 386 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 292 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 649 TYR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 711 PHE 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 861 LEU 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 1170 ILE 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 57 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 175 HIS 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 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 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 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1162 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 21 THR 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 161 THR Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 323 ASN 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 668 THR 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 843 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 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 1170 ILE Chi-restraints excluded: chain C residue 1180 GLN Chi-restraints excluded: chain C residue 1201 ASN Chi-restraints excluded: chain I residue 31 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: [321, 219, 210, 110, 225, 350, 263, 148, 159, 319, 18] chunk 321 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 350 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 148 optimal weight: 0.0060 chunk 159 optimal weight: 10.0000 chunk 319 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 881 ASN A 998 ASN A1030 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 ASN B 175 HIS B 872 ASN B1045 GLN C1001 GLN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.170060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.135034 restraints weight = 80988.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.131463 restraints weight = 58175.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.132800 restraints weight = 50627.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.133449 restraints weight = 35073.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.133506 restraints weight = 32497.594| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.8940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 32261 Z= 0.148 Angle : 0.641 16.791 44050 Z= 0.322 Chirality : 0.045 0.477 5037 Planarity : 0.004 0.045 5610 Dihedral : 5.815 114.754 4800 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 2.72 % Allowed : 19.34 % Favored : 77.94 % 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: -1.01 (0.13), residues: 3993 helix: 1.22 (0.20), residues: 758 sheet: -0.05 (0.18), residues: 838 loop : -1.62 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 676 TYR 0.027 0.002 TYR B1219 PHE 0.037 0.002 PHE A 884 TRP 0.064 0.002 TRP M 24 HIS 0.010 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (32170) covalent geometry : angle 0.63125 / 0.32 (43846) SS BOND : bond 0.00227 / 0.13 ( 69) SS BOND : angle 1.39441 / 1.06 ( 138) hydrogen bonds : bond 0.03351 / 2.18 ( 1018) hydrogen bonds : angle 4.90130 / 3.35 ( 2868) link_NAG-ASN : bond 0.00589 / 0.48 ( 22) link_NAG-ASN : angle 2.40372 / 1.89 ( 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 414 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 318 time to evaluate : 1.209 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 205 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 687 SER cc_start: 0.8402 (t) cc_final: 0.7926 (p) REVERT: A 711 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6758 (p90) REVERT: A 736 LEU cc_start: 0.8079 (mt) cc_final: 0.7818 (mp) REVERT: A 926 THR cc_start: 0.7549 (m) cc_final: 0.7054 (p) REVERT: A 994 MET cc_start: 0.8186 (mmm) cc_final: 0.7970 (mmm) REVERT: B 135 TYR cc_start: 0.4999 (OUTLIER) cc_final: 0.3352 (m-80) REVERT: B 238 MET cc_start: 0.4653 (tpp) cc_final: 0.3864 (tpp) REVERT: B 263 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8163 (ttt90) REVERT: B 344 TRP cc_start: 0.7881 (p-90) cc_final: 0.7059 (p-90) REVERT: B 609 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7165 (t80) REVERT: B 676 ARG cc_start: 0.6597 (tpt170) cc_final: 0.6377 (tpm170) REVERT: B 746 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.5515 (m-80) REVERT: B 839 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8946 (mt) REVERT: B 967 MET cc_start: 0.6024 (tmm) cc_final: 0.5784 (mmm) REVERT: B 1008 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8293 (t80) REVERT: C 851 ASP cc_start: 0.8558 (m-30) cc_final: 0.8149 (m-30) REVERT: C 934 LEU cc_start: 0.8286 (mt) cc_final: 0.8048 (mp) REVERT: C 1008 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7513 (t80) REVERT: C 1205 MET cc_start: 0.4504 (mmp) cc_final: 0.3796 (mtp) REVERT: M 45 LYS cc_start: 0.3352 (pptt) cc_final: 0.2706 (tppt) outliers start: 96 outliers final: 81 residues processed: 384 average time/residue: 0.1610 time to fit residues: 106.9983 Evaluate side-chains 391 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 302 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 649 TYR 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 861 LEU 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 1099 ILE Chi-restraints excluded: chain A residue 1170 ILE 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 175 HIS 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 314 VAL 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 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 839 ILE Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 872 ASN Chi-restraints excluded: chain B residue 972 SER Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1085 LEU Chi-restraints excluded: chain B residue 1096 ILE 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 21 THR 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 161 THR Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 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 667 TYR Chi-restraints excluded: chain C residue 668 THR 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 830 SER Chi-restraints excluded: chain C residue 843 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 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 1170 ILE Chi-restraints excluded: chain I residue 31 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: [22, 89, 311, 232, 196, 41, 243, 321, 86, 188, 231] chunk 22 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 196 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 243 optimal weight: 0.0270 chunk 321 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 872 ASN B1045 GLN C 243 ASN C 323 ASN C1001 GLN ** C1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1045 GLN ** C1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 ASN ** 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 = 0.4571 r_free = 0.4571 target = 0.170462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.136044 restraints weight = 81191.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.133072 restraints weight = 70730.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.134424 restraints weight = 53169.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.135158 restraints weight = 37759.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.135195 restraints weight = 33657.341| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.9058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32261 Z= 0.121 Angle : 0.625 17.191 44050 Z= 0.313 Chirality : 0.044 0.470 5037 Planarity : 0.004 0.052 5610 Dihedral : 5.701 111.099 4800 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 2.58 % Allowed : 19.71 % Favored : 77.72 % 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: -0.97 (0.13), residues: 3993 helix: 1.28 (0.20), residues: 763 sheet: -0.03 (0.18), residues: 846 loop : -1.61 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 676 TYR 0.023 0.001 TYR B 625 PHE 0.042 0.002 PHE B 408 TRP 0.061 0.002 TRP A 332 HIS 0.016 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (32170) covalent geometry : angle 0.61568 / 0.31 (43846) SS BOND : bond 0.00202 / 0.11 ( 69) SS BOND : angle 1.29945 / 1.00 ( 138) hydrogen bonds : bond 0.03265 / 2.11 ( 1018) hydrogen bonds : angle 4.81864 / 3.28 ( 2868) link_NAG-ASN : bond 0.00548 / 0.45 ( 22) link_NAG-ASN : angle 2.31592 / 1.83 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5920.31 seconds wall clock time: 102 minutes 57.45 seconds (6177.45 seconds total)