Starting phenix.real_space_refine on Fri May 30 09:06:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iou_35624/05_2025/8iou_35624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iou_35624/05_2025/8iou_35624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iou_35624/05_2025/8iou_35624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iou_35624/05_2025/8iou_35624.map" model { file = "/net/cci-nas-00/data/ceres_data/8iou_35624/05_2025/8iou_35624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iou_35624/05_2025/8iou_35624.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4890 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 18509 2.51 5 N 4728 2.21 5 O 5643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29013 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7892 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 53, 'TRANS': 956} Chain breaks: 7 Chain: "B" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7714 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 51, 'TRANS': 933} Chain breaks: 8 Chain: "C" Number of atoms: 7717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7717 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 52, 'TRANS': 933} Chain breaks: 8 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.90, per 1000 atoms: 0.55 Number of scatterers: 29013 At special positions: 0 Unit cell: (132.66, 141.705, 235.17, 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 133 16.00 O 5643 8.00 N 4728 7.00 C 18509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 331 " " NAG A1313 " - " ASN A 343 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN C 165 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN D 546 " " NAG M 1 " - " ASN D 90 " " NAG N 1 " - " ASN D 103 " Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 3.4 seconds 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6726 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 44 sheets defined 31.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.036A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.522A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.543A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.766A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.753A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 removed outlier: 4.165A pdb=" N THR A 827 " --> pdb=" O PHE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.220A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.687A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.942A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.291A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.567A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.612A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.966A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.289A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.875A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.652A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.135A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.671A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.913A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 removed outlier: 4.177A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.817A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.836A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.918A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.445A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.833A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.209A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.724A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.893A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.774A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.564A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.548A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.844A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 92 through 104 removed outlier: 3.554A pdb=" N LEU D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.655A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.667A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.001A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.721A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 317 removed outlier: 3.510A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.825A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.598A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.551A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.591A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 466 removed outlier: 3.802A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.734A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.830A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.562A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.627A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.584A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.930A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.769A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.930A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.061A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.716A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.609A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.858A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.564A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.702A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.663A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.744A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.093A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.575A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.117A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.559A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.157A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.530A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.530A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.683A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.510A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.770A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.989A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.673A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.949A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.712A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.178A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.663A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.626A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.891A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.037A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3201 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: 11.35 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9176 1.35 - 1.47: 7731 1.47 - 1.60: 12601 1.60 - 1.72: 0 1.72 - 1.85: 181 Bond restraints: 29689 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" C1 NAG A1313 " pdb=" O5 NAG A1313 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.08e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 ... (remaining 29684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 40268 3.51 - 7.03: 101 7.03 - 10.54: 7 10.54 - 14.05: 0 14.05 - 17.56: 1 Bond angle restraints: 40377 Sorted by residual: angle pdb=" CA PRO C 987 " pdb=" N PRO C 987 " pdb=" CD PRO C 987 " ideal model delta sigma weight residual 112.00 102.82 9.18 1.40e+00 5.10e-01 4.30e+01 angle pdb=" N ASN A 801 " pdb=" CA ASN A 801 " pdb=" CB ASN A 801 " ideal model delta sigma weight residual 110.29 118.89 -8.60 1.52e+00 4.33e-01 3.20e+01 angle pdb=" C LEU B 984 " pdb=" N ASP B 985 " pdb=" CA ASP B 985 " ideal model delta sigma weight residual 121.27 138.83 -17.56 3.40e+00 8.65e-02 2.67e+01 angle pdb=" N ASN A 343 " pdb=" CA ASN A 343 " pdb=" CB ASN A 343 " ideal model delta sigma weight residual 110.49 118.21 -7.72 1.69e+00 3.50e-01 2.09e+01 angle pdb=" N ASN A1134 " pdb=" CA ASN A1134 " pdb=" C ASN A1134 " ideal model delta sigma weight residual 108.52 114.58 -6.06 1.63e+00 3.76e-01 1.38e+01 ... (remaining 40372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.22: 17520 23.22 - 46.44: 813 46.44 - 69.67: 80 69.67 - 92.89: 30 92.89 - 116.11: 14 Dihedral angle restraints: 18457 sinusoidal: 8019 harmonic: 10438 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 20.87 72.13 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -146.69 60.69 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -136.77 50.77 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 18454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.301: 4690 0.301 - 0.601: 9 0.601 - 0.902: 3 0.902 - 1.202: 0 1.202 - 1.503: 2 Chirality restraints: 4704 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.90 -1.50 2.00e-01 2.50e+01 5.65e+01 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.17 -1.23 2.00e-01 2.50e+01 3.78e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.56e+01 ... (remaining 4701 not shown) Planarity restraints: 5176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.071 2.00e-02 2.50e+03 7.01e-02 6.14e+01 pdb=" CG ASN A 801 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.079 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.062 2.00e-02 2.50e+03 6.27e-02 4.92e+01 pdb=" CG ASN A 343 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.068 2.00e-02 2.50e+03 pdb=" C1 NAG A1313 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " 0.005 2.00e-02 2.50e+03 3.98e-02 1.98e+01 pdb=" CG ASN A 282 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.045 2.00e-02 2.50e+03 ... (remaining 5173 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2397 2.74 - 3.28: 28009 3.28 - 3.82: 45008 3.82 - 4.36: 52058 4.36 - 4.90: 93112 Nonbonded interactions: 220584 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.202 3.040 nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.215 3.120 nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASN D 90 " pdb=" N2 NAG M 1 " model vdw 2.241 3.120 nonbonded pdb=" OD2 ASP B 142 " pdb=" OG SER B 155 " model vdw 2.242 3.040 ... (remaining 220579 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 25 through 65 or resid 86 through 177 or resid 188 through \ 469 or resid 490 through 620 or resid 640 through 675 or resid 690 through 827 \ or resid 855 through 1139 or resid 1301 through 1310)) selection = (chain 'B' and (resid 25 through 65 or resid 86 through 177 or resid 188 through \ 620 or resid 640 through 1139 or resid 1301 through 1310)) selection = (chain 'C' and (resid 25 through 65 or resid 86 through 469 or resid 490 through \ 675 or resid 690 through 827 or resid 855 through 1139 or resid 1301 through 13 \ 10)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 1.250 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 62.310 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.130 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 29789 Z= 0.166 Angle : 0.696 24.069 40637 Z= 0.315 Chirality : 0.058 1.503 4704 Planarity : 0.004 0.090 5130 Dihedral : 13.110 116.109 11611 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3523 helix: 2.05 (0.17), residues: 999 sheet: 0.73 (0.20), residues: 720 loop : -1.17 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 610 HIS 0.002 0.000 HIS B 207 PHE 0.033 0.001 PHE A 802 TYR 0.013 0.001 TYR C 904 ARG 0.002 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00910 ( 46) link_NAG-ASN : angle 6.66174 ( 138) link_ALPHA1-6 : bond 0.00299 ( 1) link_ALPHA1-6 : angle 1.68049 ( 3) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 2.52479 ( 36) link_ALPHA1-3 : bond 0.00404 ( 1) link_ALPHA1-3 : angle 1.53684 ( 3) hydrogen bonds : bond 0.22280 ( 1146) hydrogen bonds : angle 7.38677 ( 3201) SS BOND : bond 0.00291 ( 40) SS BOND : angle 1.29557 ( 80) covalent geometry : bond 0.00346 (29689) covalent geometry : angle 0.57117 (40377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8577 (mp) cc_final: 0.8277 (mp) REVERT: A 133 PHE cc_start: 0.7380 (m-80) cc_final: 0.7035 (m-80) REVERT: A 177 MET cc_start: 0.4337 (ptp) cc_final: 0.4079 (ptt) REVERT: A 220 PHE cc_start: 0.7835 (t80) cc_final: 0.7632 (t80) REVERT: B 396 TYR cc_start: 0.7491 (m-80) cc_final: 0.7151 (m-10) REVERT: C 200 TYR cc_start: 0.8419 (m-80) cc_final: 0.8015 (m-80) REVERT: C 560 LEU cc_start: 0.8837 (mt) cc_final: 0.8609 (mp) REVERT: C 988 GLU cc_start: 0.7732 (mp0) cc_final: 0.7405 (mp0) REVERT: C 1010 GLN cc_start: 0.8711 (tt0) cc_final: 0.8434 (tt0) REVERT: D 270 MET cc_start: 0.2112 (tpt) cc_final: 0.1211 (tpp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3748 time to fit residues: 142.8214 Evaluate side-chains 153 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 169 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 895 GLN B 895 GLN C 207 HIS D 42 GLN D 524 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.135207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.079601 restraints weight = 69891.546| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 4.13 r_work: 0.2908 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29789 Z= 0.178 Angle : 0.676 20.537 40637 Z= 0.326 Chirality : 0.050 0.773 4704 Planarity : 0.004 0.045 5130 Dihedral : 8.753 106.893 5079 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.54 % Allowed : 4.59 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3523 helix: 2.00 (0.16), residues: 1027 sheet: 0.83 (0.19), residues: 744 loop : -1.27 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.013 0.001 HIS A 339 PHE 0.028 0.002 PHE B 906 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 46) link_NAG-ASN : angle 4.90504 ( 138) link_ALPHA1-6 : bond 0.00424 ( 1) link_ALPHA1-6 : angle 1.98752 ( 3) link_BETA1-4 : bond 0.00650 ( 12) link_BETA1-4 : angle 1.80376 ( 36) link_ALPHA1-3 : bond 0.01383 ( 1) link_ALPHA1-3 : angle 1.97185 ( 3) hydrogen bonds : bond 0.06102 ( 1146) hydrogen bonds : angle 5.38817 ( 3201) SS BOND : bond 0.00307 ( 40) SS BOND : angle 1.37886 ( 80) covalent geometry : bond 0.00415 (29689) covalent geometry : angle 0.60846 (40377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 231 ILE cc_start: 0.9009 (mm) cc_final: 0.8801 (mm) REVERT: B 495 TYR cc_start: 0.6998 (m-80) cc_final: 0.6539 (m-80) REVERT: C 200 TYR cc_start: 0.8670 (m-80) cc_final: 0.8243 (m-80) REVERT: C 242 LEU cc_start: 0.8112 (mt) cc_final: 0.7741 (mt) REVERT: C 357 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7454 (ttm-80) REVERT: C 560 LEU cc_start: 0.8850 (mt) cc_final: 0.8562 (mp) REVERT: C 1010 GLN cc_start: 0.8932 (tt0) cc_final: 0.8662 (tt0) REVERT: D 366 MET cc_start: 0.0185 (tpt) cc_final: -0.0233 (mmm) REVERT: D 557 MET cc_start: 0.6381 (tmm) cc_final: 0.5706 (ppp) REVERT: D 579 MET cc_start: 0.3603 (mtm) cc_final: 0.3297 (mtt) outliers start: 17 outliers final: 14 residues processed: 174 average time/residue: 0.3551 time to fit residues: 104.5412 Evaluate side-chains 159 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain D residue 603 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 184 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 HIS B 394 ASN D 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.134109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078385 restraints weight = 70125.684| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.13 r_work: 0.2877 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29789 Z= 0.188 Angle : 0.643 20.634 40637 Z= 0.313 Chirality : 0.049 0.658 4704 Planarity : 0.004 0.047 5130 Dihedral : 8.006 105.048 5079 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.80 % Allowed : 6.91 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3523 helix: 1.85 (0.16), residues: 1049 sheet: 0.64 (0.19), residues: 750 loop : -1.27 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 302 HIS 0.024 0.001 HIS C 207 PHE 0.027 0.002 PHE C 906 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 46) link_NAG-ASN : angle 4.37060 ( 138) link_ALPHA1-6 : bond 0.00938 ( 1) link_ALPHA1-6 : angle 1.09059 ( 3) link_BETA1-4 : bond 0.00495 ( 12) link_BETA1-4 : angle 1.72139 ( 36) link_ALPHA1-3 : bond 0.01373 ( 1) link_ALPHA1-3 : angle 1.48705 ( 3) hydrogen bonds : bond 0.05948 ( 1146) hydrogen bonds : angle 5.07878 ( 3201) SS BOND : bond 0.00293 ( 40) SS BOND : angle 1.39609 ( 80) covalent geometry : bond 0.00449 (29689) covalent geometry : angle 0.58679 (40377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7206 (m-80) cc_final: 0.6845 (m-80) REVERT: B 394 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7266 (p0) REVERT: B 396 TYR cc_start: 0.7016 (m-10) cc_final: 0.6731 (m-10) REVERT: B 495 TYR cc_start: 0.6999 (m-80) cc_final: 0.6637 (m-80) REVERT: C 200 TYR cc_start: 0.8673 (m-80) cc_final: 0.7683 (m-80) REVERT: C 242 LEU cc_start: 0.8130 (mt) cc_final: 0.7798 (mt) REVERT: C 357 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7569 (ttm-80) REVERT: C 990 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: C 1010 GLN cc_start: 0.8946 (tt0) cc_final: 0.8667 (tt0) REVERT: D 366 MET cc_start: 0.0763 (tpt) cc_final: 0.0446 (mmm) REVERT: D 557 MET cc_start: 0.6168 (tmm) cc_final: 0.5708 (ppp) REVERT: D 579 MET cc_start: 0.4086 (mtm) cc_final: 0.2231 (mmm) outliers start: 25 outliers final: 17 residues processed: 173 average time/residue: 0.3644 time to fit residues: 107.2279 Evaluate side-chains 166 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 603 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 253 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 350 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 957 GLN B 394 ASN B 901 GLN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.133760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.077394 restraints weight = 70308.407| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.80 r_work: 0.2921 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29789 Z= 0.177 Angle : 0.625 20.379 40637 Z= 0.304 Chirality : 0.048 0.605 4704 Planarity : 0.004 0.044 5130 Dihedral : 7.544 104.136 5079 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.08 % Allowed : 8.89 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3523 helix: 1.92 (0.16), residues: 1037 sheet: 0.61 (0.19), residues: 745 loop : -1.31 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS C 207 PHE 0.020 0.001 PHE B 906 TYR 0.026 0.001 TYR D 158 ARG 0.003 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 46) link_NAG-ASN : angle 4.20237 ( 138) link_ALPHA1-6 : bond 0.00922 ( 1) link_ALPHA1-6 : angle 1.91551 ( 3) link_BETA1-4 : bond 0.00449 ( 12) link_BETA1-4 : angle 1.62016 ( 36) link_ALPHA1-3 : bond 0.01461 ( 1) link_ALPHA1-3 : angle 1.84734 ( 3) hydrogen bonds : bond 0.05620 ( 1146) hydrogen bonds : angle 4.90908 ( 3201) SS BOND : bond 0.00286 ( 40) SS BOND : angle 1.31675 ( 80) covalent geometry : bond 0.00422 (29689) covalent geometry : angle 0.57144 (40377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.8175 (m-10) cc_final: 0.7956 (m-10) REVERT: B 427 ASP cc_start: 0.8113 (m-30) cc_final: 0.7901 (p0) REVERT: B 495 TYR cc_start: 0.7024 (m-80) cc_final: 0.6712 (m-80) REVERT: C 200 TYR cc_start: 0.8642 (m-80) cc_final: 0.8180 (m-80) REVERT: C 357 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7626 (ttm-80) REVERT: C 990 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: C 1010 GLN cc_start: 0.8899 (tt0) cc_final: 0.8638 (tt0) REVERT: D 366 MET cc_start: 0.0763 (tpt) cc_final: 0.0403 (mmm) REVERT: D 557 MET cc_start: 0.6110 (tmm) cc_final: 0.5836 (ppp) outliers start: 34 outliers final: 18 residues processed: 177 average time/residue: 0.3456 time to fit residues: 105.8292 Evaluate side-chains 160 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 603 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 49 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 299 optimal weight: 30.0000 chunk 13 optimal weight: 0.7980 chunk 305 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.134088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073815 restraints weight = 69933.547| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.09 r_work: 0.2949 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29789 Z= 0.151 Angle : 0.605 20.166 40637 Z= 0.293 Chirality : 0.047 0.564 4704 Planarity : 0.004 0.044 5130 Dihedral : 7.256 104.472 5079 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.24 % Allowed : 9.71 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3523 helix: 1.95 (0.16), residues: 1037 sheet: 0.67 (0.19), residues: 740 loop : -1.28 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 PHE 0.019 0.001 PHE A 135 TYR 0.018 0.001 TYR A 351 ARG 0.009 0.000 ARG D 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 46) link_NAG-ASN : angle 4.08537 ( 138) link_ALPHA1-6 : bond 0.00862 ( 1) link_ALPHA1-6 : angle 1.51086 ( 3) link_BETA1-4 : bond 0.00426 ( 12) link_BETA1-4 : angle 1.53380 ( 36) link_ALPHA1-3 : bond 0.01290 ( 1) link_ALPHA1-3 : angle 1.69621 ( 3) hydrogen bonds : bond 0.05258 ( 1146) hydrogen bonds : angle 4.79359 ( 3201) SS BOND : bond 0.00297 ( 40) SS BOND : angle 1.26792 ( 80) covalent geometry : bond 0.00355 (29689) covalent geometry : angle 0.55315 (40377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 3.086 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.7253 (p90) cc_final: 0.7046 (p90) REVERT: B 421 TYR cc_start: 0.8234 (m-10) cc_final: 0.7966 (m-10) REVERT: B 495 TYR cc_start: 0.7124 (m-80) cc_final: 0.6822 (m-80) REVERT: C 200 TYR cc_start: 0.8654 (m-80) cc_final: 0.8253 (m-80) REVERT: C 314 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8612 (tp40) REVERT: C 990 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: C 1010 GLN cc_start: 0.9016 (tt0) cc_final: 0.8799 (tt0) REVERT: D 45 LEU cc_start: 0.8367 (pp) cc_final: 0.8135 (tp) REVERT: D 323 MET cc_start: 0.4518 (tpt) cc_final: 0.4147 (tpp) REVERT: D 366 MET cc_start: 0.0914 (tpt) cc_final: 0.0521 (mmm) REVERT: D 557 MET cc_start: 0.6235 (tmm) cc_final: 0.6031 (ppp) REVERT: D 579 MET cc_start: 0.4437 (mtm) cc_final: 0.4031 (mtt) outliers start: 39 outliers final: 24 residues processed: 178 average time/residue: 0.3474 time to fit residues: 106.9728 Evaluate side-chains 173 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 603 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 231 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073051 restraints weight = 70203.531| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.08 r_work: 0.2933 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29789 Z= 0.174 Angle : 0.618 20.228 40637 Z= 0.300 Chirality : 0.048 0.535 4704 Planarity : 0.004 0.045 5130 Dihedral : 7.079 104.195 5079 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.27 % Allowed : 10.41 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3523 helix: 1.94 (0.16), residues: 1033 sheet: 0.62 (0.19), residues: 708 loop : -1.29 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.014 0.001 PHE B1121 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 46) link_NAG-ASN : angle 4.05305 ( 138) link_ALPHA1-6 : bond 0.00855 ( 1) link_ALPHA1-6 : angle 1.49539 ( 3) link_BETA1-4 : bond 0.00402 ( 12) link_BETA1-4 : angle 1.51967 ( 36) link_ALPHA1-3 : bond 0.01344 ( 1) link_ALPHA1-3 : angle 1.59112 ( 3) hydrogen bonds : bond 0.05471 ( 1146) hydrogen bonds : angle 4.79674 ( 3201) SS BOND : bond 0.00277 ( 40) SS BOND : angle 1.44179 ( 80) covalent geometry : bond 0.00417 (29689) covalent geometry : angle 0.56728 (40377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.5563 (t80) REVERT: B 421 TYR cc_start: 0.8239 (m-10) cc_final: 0.8006 (m-10) REVERT: B 424 LYS cc_start: 0.8525 (tppt) cc_final: 0.8149 (mmtp) REVERT: B 495 TYR cc_start: 0.7156 (m-80) cc_final: 0.6812 (m-80) REVERT: B 985 ASP cc_start: 0.8598 (t0) cc_final: 0.8145 (t70) REVERT: C 200 TYR cc_start: 0.8654 (m-80) cc_final: 0.8312 (m-80) REVERT: C 314 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8634 (tp40) REVERT: C 546 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6738 (mt) REVERT: C 1010 GLN cc_start: 0.9017 (tt0) cc_final: 0.8799 (tt0) REVERT: D 366 MET cc_start: 0.1013 (tpt) cc_final: 0.0629 (mmm) REVERT: D 383 MET cc_start: 0.1495 (tmm) cc_final: 0.1015 (mtt) REVERT: D 579 MET cc_start: 0.4674 (mtm) cc_final: 0.4230 (mtt) outliers start: 40 outliers final: 27 residues processed: 174 average time/residue: 0.3528 time to fit residues: 105.0197 Evaluate side-chains 172 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 603 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 194 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 208 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.134003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074498 restraints weight = 70314.720| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.09 r_work: 0.2947 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29789 Z= 0.138 Angle : 0.594 19.866 40637 Z= 0.286 Chirality : 0.047 0.523 4704 Planarity : 0.004 0.044 5130 Dihedral : 6.822 104.373 5079 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.40 % Allowed : 10.54 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3523 helix: 2.06 (0.16), residues: 1024 sheet: 0.72 (0.20), residues: 709 loop : -1.21 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 PHE 0.017 0.001 PHE A 133 TYR 0.017 0.001 TYR A1067 ARG 0.010 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 46) link_NAG-ASN : angle 3.96298 ( 138) link_ALPHA1-6 : bond 0.00960 ( 1) link_ALPHA1-6 : angle 1.48466 ( 3) link_BETA1-4 : bond 0.00400 ( 12) link_BETA1-4 : angle 1.47878 ( 36) link_ALPHA1-3 : bond 0.01130 ( 1) link_ALPHA1-3 : angle 1.53898 ( 3) hydrogen bonds : bond 0.04963 ( 1146) hydrogen bonds : angle 4.65297 ( 3201) SS BOND : bond 0.00292 ( 40) SS BOND : angle 1.27734 ( 80) covalent geometry : bond 0.00323 (29689) covalent geometry : angle 0.54428 (40377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.5498 (OUTLIER) cc_final: 0.5239 (t80) REVERT: B 421 TYR cc_start: 0.8199 (m-10) cc_final: 0.7984 (m-10) REVERT: B 424 LYS cc_start: 0.8492 (tppt) cc_final: 0.8092 (mmtp) REVERT: B 495 TYR cc_start: 0.7211 (m-80) cc_final: 0.6921 (m-80) REVERT: B 985 ASP cc_start: 0.8616 (t0) cc_final: 0.8173 (t70) REVERT: C 314 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8642 (tp40) REVERT: C 546 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6719 (mt) REVERT: C 1010 GLN cc_start: 0.9006 (tt0) cc_final: 0.8790 (tt0) REVERT: D 366 MET cc_start: 0.1054 (tpt) cc_final: 0.0673 (mmm) REVERT: D 383 MET cc_start: 0.1633 (tmm) cc_final: 0.1179 (mtt) REVERT: D 557 MET cc_start: 0.6529 (tmm) cc_final: 0.5670 (ppp) REVERT: D 579 MET cc_start: 0.4662 (mtm) cc_final: 0.4208 (mtt) outliers start: 44 outliers final: 31 residues processed: 180 average time/residue: 0.3550 time to fit residues: 111.0139 Evaluate side-chains 179 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 330 optimal weight: 0.0980 chunk 200 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 243 optimal weight: 0.3980 chunk 332 optimal weight: 7.9990 chunk 339 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 109 optimal weight: 0.0770 chunk 135 optimal weight: 6.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.134956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075097 restraints weight = 70740.870| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.05 r_work: 0.2984 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29789 Z= 0.102 Angle : 0.572 19.319 40637 Z= 0.275 Chirality : 0.046 0.501 4704 Planarity : 0.004 0.054 5130 Dihedral : 6.448 104.279 5079 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.05 % Allowed : 10.92 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3523 helix: 2.22 (0.17), residues: 1014 sheet: 0.82 (0.20), residues: 705 loop : -1.14 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.004 0.000 HIS B 207 PHE 0.025 0.001 PHE B 201 TYR 0.016 0.001 TYR A1067 ARG 0.009 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 46) link_NAG-ASN : angle 3.82912 ( 138) link_ALPHA1-6 : bond 0.00944 ( 1) link_ALPHA1-6 : angle 1.45280 ( 3) link_BETA1-4 : bond 0.00411 ( 12) link_BETA1-4 : angle 1.42581 ( 36) link_ALPHA1-3 : bond 0.00973 ( 1) link_ALPHA1-3 : angle 1.52866 ( 3) hydrogen bonds : bond 0.04285 ( 1146) hydrogen bonds : angle 4.49552 ( 3201) SS BOND : bond 0.00271 ( 40) SS BOND : angle 1.07490 ( 80) covalent geometry : bond 0.00217 (29689) covalent geometry : angle 0.52424 (40377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.5736 (OUTLIER) cc_final: 0.5513 (t80) REVERT: B 424 LYS cc_start: 0.8510 (tppt) cc_final: 0.8095 (mmtp) REVERT: B 495 TYR cc_start: 0.7195 (m-80) cc_final: 0.6911 (m-80) REVERT: C 177 MET cc_start: 0.7097 (pmm) cc_final: 0.6790 (pmm) REVERT: C 314 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8633 (tp40) REVERT: C 1010 GLN cc_start: 0.8990 (tt0) cc_final: 0.8757 (tt0) REVERT: D 366 MET cc_start: 0.0982 (tpt) cc_final: 0.0446 (mmm) REVERT: D 383 MET cc_start: 0.1572 (tmm) cc_final: 0.1116 (mtt) REVERT: D 557 MET cc_start: 0.6315 (tmm) cc_final: 0.5517 (ppp) REVERT: D 579 MET cc_start: 0.4084 (mtm) cc_final: 0.3611 (mtt) outliers start: 33 outliers final: 25 residues processed: 172 average time/residue: 0.3504 time to fit residues: 104.5213 Evaluate side-chains 170 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 281 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 117 optimal weight: 0.0370 chunk 234 optimal weight: 2.9990 chunk 297 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.134575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074631 restraints weight = 70876.460| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.07 r_work: 0.2945 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29789 Z= 0.118 Angle : 0.576 19.400 40637 Z= 0.278 Chirality : 0.046 0.508 4704 Planarity : 0.004 0.053 5130 Dihedral : 6.251 103.966 5079 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.02 % Allowed : 11.21 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3523 helix: 2.21 (0.17), residues: 1015 sheet: 0.86 (0.20), residues: 708 loop : -1.13 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS B 207 PHE 0.038 0.001 PHE A 133 TYR 0.016 0.001 TYR A1067 ARG 0.008 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 46) link_NAG-ASN : angle 3.82494 ( 138) link_ALPHA1-6 : bond 0.00869 ( 1) link_ALPHA1-6 : angle 1.47993 ( 3) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 1.44669 ( 36) link_ALPHA1-3 : bond 0.01181 ( 1) link_ALPHA1-3 : angle 1.64337 ( 3) hydrogen bonds : bond 0.04455 ( 1146) hydrogen bonds : angle 4.47653 ( 3201) SS BOND : bond 0.00268 ( 40) SS BOND : angle 1.14231 ( 80) covalent geometry : bond 0.00267 (29689) covalent geometry : angle 0.52863 (40377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.5480 (t80) REVERT: B 392 PHE cc_start: 0.8415 (m-80) cc_final: 0.8120 (m-80) REVERT: B 424 LYS cc_start: 0.8474 (tppt) cc_final: 0.8064 (mmtp) REVERT: B 434 ILE cc_start: 0.8223 (mp) cc_final: 0.7713 (pt) REVERT: B 495 TYR cc_start: 0.7200 (m-80) cc_final: 0.6903 (m-80) REVERT: B 514 SER cc_start: 0.8907 (t) cc_final: 0.8700 (t) REVERT: C 177 MET cc_start: 0.7072 (pmm) cc_final: 0.6768 (pmm) REVERT: C 200 TYR cc_start: 0.8649 (m-80) cc_final: 0.8370 (m-80) REVERT: C 314 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8633 (tp40) REVERT: C 990 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: C 1010 GLN cc_start: 0.9028 (tt0) cc_final: 0.8788 (tt0) REVERT: D 366 MET cc_start: 0.0960 (tpt) cc_final: 0.0386 (tpt) REVERT: D 383 MET cc_start: 0.1667 (tmm) cc_final: 0.1247 (mtt) REVERT: D 408 MET cc_start: 0.5628 (OUTLIER) cc_final: 0.5398 (mmm) REVERT: D 557 MET cc_start: 0.6381 (tmm) cc_final: 0.5616 (ppp) REVERT: D 579 MET cc_start: 0.4125 (mtm) cc_final: 0.3657 (mtt) outliers start: 32 outliers final: 26 residues processed: 168 average time/residue: 0.3463 time to fit residues: 101.1407 Evaluate side-chains 175 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 183 optimal weight: 0.7980 chunk 347 optimal weight: 50.0000 chunk 45 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 35 optimal weight: 50.0000 chunk 76 optimal weight: 0.8980 chunk 317 optimal weight: 8.9990 chunk 177 optimal weight: 0.6980 chunk 315 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.134434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074401 restraints weight = 70631.558| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.09 r_work: 0.2940 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29789 Z= 0.121 Angle : 0.574 19.302 40637 Z= 0.278 Chirality : 0.046 0.512 4704 Planarity : 0.004 0.054 5130 Dihedral : 6.159 103.797 5079 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.99 % Allowed : 11.37 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3523 helix: 2.20 (0.17), residues: 1015 sheet: 0.86 (0.20), residues: 708 loop : -1.11 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 PHE 0.024 0.001 PHE A 135 TYR 0.016 0.001 TYR A1067 ARG 0.007 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 46) link_NAG-ASN : angle 3.78770 ( 138) link_ALPHA1-6 : bond 0.01047 ( 1) link_ALPHA1-6 : angle 1.58996 ( 3) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 1.43824 ( 36) link_ALPHA1-3 : bond 0.00928 ( 1) link_ALPHA1-3 : angle 1.41443 ( 3) hydrogen bonds : bond 0.04554 ( 1146) hydrogen bonds : angle 4.47210 ( 3201) SS BOND : bond 0.00268 ( 40) SS BOND : angle 1.15678 ( 80) covalent geometry : bond 0.00278 (29689) covalent geometry : angle 0.52725 (40377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7046 Ramachandran restraints generated. 3523 Oldfield, 0 Emsley, 3523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.8480 (tppt) cc_final: 0.8049 (mmtp) REVERT: B 434 ILE cc_start: 0.8270 (mp) cc_final: 0.7786 (pt) REVERT: B 495 TYR cc_start: 0.7207 (m-80) cc_final: 0.6918 (m-80) REVERT: B 514 SER cc_start: 0.8860 (t) cc_final: 0.8653 (t) REVERT: B 1092 GLU cc_start: 0.8884 (pm20) cc_final: 0.8426 (mp0) REVERT: C 177 MET cc_start: 0.7012 (pmm) cc_final: 0.6691 (pmm) REVERT: C 200 TYR cc_start: 0.8595 (m-80) cc_final: 0.8321 (m-80) REVERT: C 314 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8646 (tp40) REVERT: C 990 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: C 1010 GLN cc_start: 0.9020 (tt0) cc_final: 0.8813 (tt0) REVERT: D 366 MET cc_start: 0.0899 (tpt) cc_final: 0.0392 (tpt) REVERT: D 383 MET cc_start: 0.1756 (tmm) cc_final: 0.1371 (mtt) REVERT: D 557 MET cc_start: 0.6472 (tmm) cc_final: 0.5713 (ppp) REVERT: D 579 MET cc_start: 0.4245 (mtm) cc_final: 0.3778 (mtt) outliers start: 31 outliers final: 26 residues processed: 169 average time/residue: 0.3522 time to fit residues: 104.1194 Evaluate side-chains 171 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 25 optimal weight: 0.0070 chunk 79 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 274 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 353 optimal weight: 2.9990 chunk 260 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.135438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.078420 restraints weight = 70758.240| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.45 r_work: 0.2986 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29789 Z= 0.099 Angle : 0.553 18.946 40637 Z= 0.268 Chirality : 0.045 0.497 4704 Planarity : 0.004 0.055 5130 Dihedral : 5.983 103.760 5079 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.99 % Allowed : 11.43 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3523 helix: 2.29 (0.17), residues: 1013 sheet: 0.90 (0.20), residues: 710 loop : -1.05 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.000 HIS B 207 PHE 0.037 0.001 PHE A 135 TYR 0.015 0.001 TYR A1067 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 46) link_NAG-ASN : angle 3.65282 ( 138) link_ALPHA1-6 : bond 0.01075 ( 1) link_ALPHA1-6 : angle 1.58082 ( 3) link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 1.40385 ( 36) link_ALPHA1-3 : bond 0.00864 ( 1) link_ALPHA1-3 : angle 1.43199 ( 3) hydrogen bonds : bond 0.04007 ( 1146) hydrogen bonds : angle 4.38317 ( 3201) SS BOND : bond 0.00249 ( 40) SS BOND : angle 0.97949 ( 80) covalent geometry : bond 0.00212 (29689) covalent geometry : angle 0.50811 (40377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22979.61 seconds wall clock time: 394 minutes 52.14 seconds (23692.14 seconds total)