Starting phenix.real_space_refine on Fri Mar 22 15:18:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iou_35624/03_2024/8iou_35624.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iou_35624/03_2024/8iou_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iou_35624/03_2024/8iou_35624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iou_35624/03_2024/8iou_35624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iou_35624/03_2024/8iou_35624.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iou_35624/03_2024/8iou_35624.pdb" } 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 Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 14.89, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 11.09 Conformation dependent library (CDL) restraints added in 5.4 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: 3.40 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: 11.59 Time building geometry restraints manager: 12.07 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: 99.17 - 107.11: 951 107.11 - 115.04: 17866 115.04 - 122.97: 19095 122.97 - 130.90: 2369 130.90 - 138.83: 96 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 2.440 nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.215 2.520 nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASN D 90 " pdb=" N2 NAG M 1 " model vdw 2.241 2.520 nonbonded pdb=" OD2 ASP B 142 " pdb=" OG SER B 155 " model vdw 2.242 2.440 ... (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 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 13.560 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 75.200 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.200 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.620 ------------------------------------------------------------------------------- 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 29689 Z= 0.225 Angle : 0.571 17.563 40377 Z= 0.285 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 3.556 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: 0.3852 time to fit residues: 146.4147 Evaluate side-chains 153 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.126 ------------------------------------------------------------------------------- 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: 1.9990 chunk 269 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 323 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 613 GLN D 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29689 Z= 0.327 Angle : 0.616 12.626 40377 Z= 0.315 Chirality : 0.050 0.780 4704 Planarity : 0.004 0.045 5130 Dihedral : 8.874 106.801 5079 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.64 % Allowed : 5.16 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3523 helix: 1.94 (0.16), residues: 1028 sheet: 0.69 (0.19), residues: 760 loop : -1.31 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.012 0.001 HIS A 339 PHE 0.034 0.002 PHE B 906 TYR 0.021 0.001 TYR A1067 ARG 0.003 0.000 ARG C1107 *********************** 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 184 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 231 ILE cc_start: 0.8983 (mm) cc_final: 0.8751 (mm) REVERT: C 200 TYR cc_start: 0.8542 (m-80) cc_final: 0.8161 (m-80) REVERT: C 242 LEU cc_start: 0.8104 (mt) cc_final: 0.7771 (mt) REVERT: C 560 LEU cc_start: 0.8895 (mt) cc_final: 0.8604 (mp) REVERT: C 1010 GLN cc_start: 0.8746 (tt0) cc_final: 0.8459 (tt0) REVERT: D 366 MET cc_start: -0.0417 (tpt) cc_final: -0.0682 (mmp) REVERT: D 480 MET cc_start: 0.3279 (ptt) cc_final: 0.2641 (ptt) outliers start: 20 outliers final: 15 residues processed: 175 average time/residue: 0.3592 time to fit residues: 107.0480 Evaluate side-chains 161 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 2.893 ------------------------------------------------------------------------------- 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 339 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 428 ASP 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 C residue 511 VAL 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 179 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 269 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 323 optimal weight: 0.5980 chunk 349 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 321 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 394 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29689 Z= 0.178 Angle : 0.537 11.879 40377 Z= 0.272 Chirality : 0.047 0.685 4704 Planarity : 0.004 0.045 5130 Dihedral : 7.904 105.891 5079 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.70 % Allowed : 7.17 % Favored : 92.13 % 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: 0.32 (0.14), residues: 3523 helix: 2.09 (0.16), residues: 1028 sheet: 0.85 (0.19), residues: 744 loop : -1.29 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 478 HIS 0.019 0.001 HIS A 339 PHE 0.019 0.001 PHE A 168 TYR 0.017 0.001 TYR A1067 ARG 0.006 0.000 ARG C 357 *********************** 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 185 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7230 (m-80) cc_final: 0.6874 (m-80) REVERT: B 394 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7335 (p0) REVERT: C 200 TYR cc_start: 0.8483 (m-80) cc_final: 0.8177 (m-80) REVERT: C 242 LEU cc_start: 0.8171 (mt) cc_final: 0.7888 (mt) REVERT: C 990 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: C 1010 GLN cc_start: 0.8729 (tt0) cc_final: 0.8439 (tt0) REVERT: D 152 MET cc_start: 0.2273 (ptt) cc_final: 0.2066 (ptp) REVERT: D 190 MET cc_start: 0.4200 (ppp) cc_final: 0.3881 (ppp) outliers start: 22 outliers final: 13 residues processed: 176 average time/residue: 0.3592 time to fit residues: 107.3520 Evaluate side-chains 164 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 1096 VAL 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 220 PHE 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 603 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 40.0000 chunk 243 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 325 optimal weight: 0.9990 chunk 344 optimal weight: 20.0000 chunk 169 optimal weight: 0.0670 chunk 308 optimal weight: 10.0000 chunk 92 optimal weight: 0.0030 overall best weight: 0.9332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN D 277 ASN D 524 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29689 Z= 0.158 Angle : 0.516 10.391 40377 Z= 0.260 Chirality : 0.046 0.618 4704 Planarity : 0.004 0.044 5130 Dihedral : 7.205 105.049 5079 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.92 % Allowed : 8.57 % Favored : 90.51 % 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: 0.41 (0.14), residues: 3523 helix: 2.20 (0.17), residues: 1027 sheet: 0.88 (0.19), residues: 745 loop : -1.25 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 478 HIS 0.006 0.001 HIS C 207 PHE 0.015 0.001 PHE A 168 TYR 0.016 0.001 TYR A 351 ARG 0.005 0.000 ARG C 357 *********************** 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 190 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.8115 (m-10) cc_final: 0.7890 (m-10) REVERT: C 242 LEU cc_start: 0.8274 (mt) cc_final: 0.7969 (mt) REVERT: C 990 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: C 1010 GLN cc_start: 0.8706 (tt0) cc_final: 0.8432 (tt0) outliers start: 29 outliers final: 20 residues processed: 180 average time/residue: 0.3398 time to fit residues: 105.7890 Evaluate side-chains 166 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 3.533 ------------------------------------------------------------------------------- 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 565 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 428 ASP 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 869 MET Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL 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 603 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 293 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 450 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29689 Z= 0.320 Angle : 0.595 11.140 40377 Z= 0.302 Chirality : 0.048 0.561 4704 Planarity : 0.004 0.044 5130 Dihedral : 7.050 103.882 5079 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.21 % Allowed : 9.62 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3523 helix: 1.94 (0.16), residues: 1030 sheet: 0.70 (0.20), residues: 720 loop : -1.31 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.006 0.001 HIS C 207 PHE 0.028 0.002 PHE B 906 TYR 0.019 0.002 TYR A1067 ARG 0.006 0.000 ARG C 357 *********************** 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 fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.8161 (m-10) cc_final: 0.7927 (m-10) REVERT: B 424 LYS cc_start: 0.8489 (tppt) cc_final: 0.8122 (mmtp) REVERT: B 985 ASP cc_start: 0.8558 (t0) cc_final: 0.8150 (t70) REVERT: C 200 TYR cc_start: 0.8367 (m-80) cc_final: 0.8030 (m-80) REVERT: C 990 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7043 (pm20) REVERT: C 1010 GLN cc_start: 0.8737 (tt0) cc_final: 0.8504 (tt0) REVERT: D 366 MET cc_start: 0.0900 (mmp) cc_final: 0.0633 (mmm) REVERT: D 383 MET cc_start: 0.1176 (tmm) cc_final: -0.0592 (mtt) outliers start: 38 outliers final: 24 residues processed: 178 average time/residue: 0.3552 time to fit residues: 108.2609 Evaluate side-chains 173 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 2.906 ------------------------------------------------------------------------------- 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 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 428 ASP 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 370 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 943 SER 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 579 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 115 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 285 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29689 Z= 0.336 Angle : 0.588 9.854 40377 Z= 0.300 Chirality : 0.048 0.560 4704 Planarity : 0.004 0.044 5130 Dihedral : 6.885 103.566 5079 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.40 % Allowed : 10.61 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3523 helix: 1.92 (0.16), residues: 1031 sheet: 0.56 (0.19), residues: 720 loop : -1.36 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 886 HIS 0.006 0.001 HIS C 207 PHE 0.022 0.002 PHE A 135 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG C 905 *********************** 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 191 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.8201 (m-10) cc_final: 0.7897 (m-10) REVERT: B 423 TYR cc_start: 0.6899 (t80) cc_final: 0.6671 (t80) REVERT: B 424 LYS cc_start: 0.8500 (tppt) cc_final: 0.8160 (mmtp) REVERT: B 495 TYR cc_start: 0.7082 (m-80) cc_final: 0.6802 (m-80) REVERT: B 985 ASP cc_start: 0.8653 (t0) cc_final: 0.8104 (t0) REVERT: C 200 TYR cc_start: 0.8317 (m-80) cc_final: 0.8025 (m-80) REVERT: C 314 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8487 (tp40) REVERT: C 546 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6963 (mt) REVERT: C 990 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: C 1010 GLN cc_start: 0.8754 (tt0) cc_final: 0.8522 (tt0) REVERT: D 270 MET cc_start: 0.1255 (tpt) cc_final: 0.0753 (tpt) REVERT: D 366 MET cc_start: 0.1243 (mmp) cc_final: 0.0995 (mmm) REVERT: D 383 MET cc_start: 0.1373 (tmm) cc_final: -0.0198 (mtt) outliers start: 44 outliers final: 31 residues processed: 178 average time/residue: 0.3565 time to fit residues: 109.7248 Evaluate side-chains 176 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE 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 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 468 ILE 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 943 SER 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 45 LEU Chi-restraints excluded: chain D residue 332 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 332 optimal weight: 20.0000 chunk 38 optimal weight: 0.0970 chunk 196 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 289 optimal weight: 0.2980 chunk 192 optimal weight: 0.0870 chunk 343 optimal weight: 5.9990 chunk 214 optimal weight: 0.0070 chunk 209 optimal weight: 4.9990 chunk 158 optimal weight: 0.0870 overall best weight: 0.1152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29689 Z= 0.129 Angle : 0.502 9.076 40377 Z= 0.254 Chirality : 0.045 0.542 4704 Planarity : 0.004 0.044 5130 Dihedral : 6.443 104.140 5079 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.96 % Allowed : 11.37 % Favored : 87.68 % 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: 2.26 (0.17), residues: 1013 sheet: 0.82 (0.19), residues: 740 loop : -1.21 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.000 HIS B 207 PHE 0.023 0.001 PHE A 135 TYR 0.015 0.001 TYR A1067 ARG 0.005 0.000 ARG D 245 *********************** 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 186 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.8080 (m-10) cc_final: 0.7809 (m-10) REVERT: B 423 TYR cc_start: 0.6869 (t80) cc_final: 0.6588 (t80) REVERT: B 424 LYS cc_start: 0.8397 (tppt) cc_final: 0.8023 (mmtp) REVERT: B 985 ASP cc_start: 0.8570 (t0) cc_final: 0.8149 (t70) REVERT: C 177 MET cc_start: 0.7113 (pmm) cc_final: 0.6800 (pmm) REVERT: C 200 TYR cc_start: 0.8230 (m-80) cc_final: 0.7935 (m-80) REVERT: C 314 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8480 (tp40) REVERT: C 1010 GLN cc_start: 0.8686 (tt0) cc_final: 0.8412 (tt0) REVERT: D 270 MET cc_start: 0.1163 (OUTLIER) cc_final: 0.0719 (tpt) REVERT: D 383 MET cc_start: 0.1139 (tmm) cc_final: -0.0178 (mtt) outliers start: 30 outliers final: 20 residues processed: 176 average time/residue: 0.3634 time to fit residues: 109.8012 Evaluate side-chains 173 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 177 MET 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 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 294 ASP 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 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 546 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 332 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 0.0980 chunk 137 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 103 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 233 optimal weight: 6.9990 chunk 169 optimal weight: 0.0010 chunk 31 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 overall best weight: 0.5466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29689 Z= 0.130 Angle : 0.498 10.944 40377 Z= 0.250 Chirality : 0.045 0.494 4704 Planarity : 0.004 0.045 5130 Dihedral : 6.234 103.683 5079 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.99 % Allowed : 11.75 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3523 helix: 2.34 (0.17), residues: 1006 sheet: 0.89 (0.20), residues: 710 loop : -1.15 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.003 0.000 HIS B 207 PHE 0.031 0.001 PHE B 201 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG A1107 *********************** 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 187 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 2.754 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8671 (mm) cc_final: 0.8462 (tp) REVERT: B 241 LEU cc_start: 0.8558 (mp) cc_final: 0.7898 (pp) REVERT: B 421 TYR cc_start: 0.8094 (m-10) cc_final: 0.7819 (m-10) REVERT: B 423 TYR cc_start: 0.6861 (t80) cc_final: 0.6623 (t80) REVERT: B 424 LYS cc_start: 0.8395 (tppt) cc_final: 0.7996 (mmtp) REVERT: B 434 ILE cc_start: 0.8141 (mp) cc_final: 0.7702 (pt) REVERT: B 985 ASP cc_start: 0.8526 (t0) cc_final: 0.8131 (t70) REVERT: C 177 MET cc_start: 0.7065 (pmm) cc_final: 0.6745 (pmm) REVERT: C 314 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8465 (tp40) REVERT: C 1010 GLN cc_start: 0.8688 (tt0) cc_final: 0.8429 (tt0) REVERT: D 82 MET cc_start: 0.5258 (ptt) cc_final: 0.4893 (ptt) REVERT: D 190 MET cc_start: 0.3322 (ppp) cc_final: 0.2892 (ppp) REVERT: D 270 MET cc_start: 0.1177 (tpt) cc_final: 0.0706 (tpt) REVERT: D 366 MET cc_start: 0.0740 (mmp) cc_final: 0.0182 (mmm) REVERT: D 383 MET cc_start: 0.1139 (tmm) cc_final: -0.0060 (mtt) outliers start: 31 outliers final: 24 residues processed: 176 average time/residue: 0.3643 time to fit residues: 110.4896 Evaluate side-chains 174 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 177 MET 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 1104 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 294 ASP 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 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 468 ILE 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 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 20.0000 chunk 328 optimal weight: 0.1980 chunk 299 optimal weight: 7.9990 chunk 319 optimal weight: 30.0000 chunk 192 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 chunk 318 optimal weight: 10.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29689 Z= 0.301 Angle : 0.566 8.671 40377 Z= 0.288 Chirality : 0.047 0.532 4704 Planarity : 0.004 0.044 5130 Dihedral : 6.446 102.489 5079 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.99 % Allowed : 12.04 % Favored : 86.97 % 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: 0.31 (0.14), residues: 3523 helix: 2.14 (0.17), residues: 1003 sheet: 0.77 (0.20), residues: 701 loop : -1.20 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 886 HIS 0.005 0.001 HIS A1064 PHE 0.032 0.002 PHE B 392 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG A1107 *********************** 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 178 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.8126 (m-10) cc_final: 0.7865 (m-10) REVERT: B 424 LYS cc_start: 0.8492 (tppt) cc_final: 0.8056 (mmtp) REVERT: B 985 ASP cc_start: 0.8571 (t0) cc_final: 0.8167 (t70) REVERT: C 200 TYR cc_start: 0.8303 (m-80) cc_final: 0.7502 (m-80) REVERT: C 314 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: C 546 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6899 (mt) REVERT: C 1010 GLN cc_start: 0.8739 (tt0) cc_final: 0.8499 (tt0) REVERT: D 366 MET cc_start: 0.0586 (mmp) cc_final: 0.0356 (mmm) REVERT: D 383 MET cc_start: 0.1313 (tmm) cc_final: 0.0173 (mtt) outliers start: 31 outliers final: 24 residues processed: 168 average time/residue: 0.3426 time to fit residues: 99.1665 Evaluate side-chains 171 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 177 MET 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 705 VAL 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 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 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 468 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 895 GLN 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 45 LEU Chi-restraints excluded: chain D residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.0030 chunk 338 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 354 optimal weight: 5.9990 chunk 326 optimal weight: 5.9990 chunk 282 optimal weight: 0.0970 chunk 29 optimal weight: 8.9990 chunk 218 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29689 Z= 0.232 Angle : 0.537 8.918 40377 Z= 0.272 Chirality : 0.046 0.518 4704 Planarity : 0.004 0.044 5130 Dihedral : 6.372 102.764 5079 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.05 % Allowed : 12.20 % Favored : 86.75 % 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: 0.30 (0.14), residues: 3523 helix: 2.13 (0.17), residues: 1015 sheet: 0.71 (0.20), residues: 702 loop : -1.20 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 886 HIS 0.003 0.001 HIS D 493 PHE 0.035 0.001 PHE A 135 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG A1107 ********************** 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 180 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 421 TYR cc_start: 0.8126 (m-10) cc_final: 0.7850 (m-10) REVERT: B 424 LYS cc_start: 0.8462 (tppt) cc_final: 0.8043 (mmtp) REVERT: B 985 ASP cc_start: 0.8632 (t0) cc_final: 0.8193 (t70) REVERT: B 1092 GLU cc_start: 0.8642 (pm20) cc_final: 0.8200 (mp0) REVERT: C 314 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8527 (tp40) REVERT: C 546 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6789 (mt) REVERT: C 1010 GLN cc_start: 0.8732 (tt0) cc_final: 0.8474 (tt0) REVERT: D 190 MET cc_start: 0.2892 (ppp) cc_final: 0.2469 (ppp) REVERT: D 383 MET cc_start: 0.1007 (tmm) cc_final: 0.0224 (mtt) outliers start: 33 outliers final: 25 residues processed: 171 average time/residue: 0.3633 time to fit residues: 106.5725 Evaluate side-chains 174 residues out of total 3140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 386 LYS 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 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 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 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 468 ILE 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 45 LEU Chi-restraints excluded: chain D residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 4.9990 chunk 300 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 282 optimal weight: 0.0980 chunk 118 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.133728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073923 restraints weight = 70680.297| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.02 r_work: 0.2956 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29689 Z= 0.212 Angle : 0.526 9.009 40377 Z= 0.267 Chirality : 0.046 0.512 4704 Planarity : 0.004 0.044 5130 Dihedral : 6.275 102.851 5079 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.96 % Allowed : 12.29 % Favored : 86.75 % 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: 0.34 (0.14), residues: 3523 helix: 2.18 (0.17), residues: 1010 sheet: 0.73 (0.20), residues: 702 loop : -1.18 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 PHE 0.031 0.001 PHE A 135 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6184.98 seconds wall clock time: 112 minutes 26.72 seconds (6746.72 seconds total)