Starting phenix.real_space_refine on Wed May 28 20:49:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xuz_38687/05_2025/8xuz_38687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xuz_38687/05_2025/8xuz_38687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xuz_38687/05_2025/8xuz_38687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xuz_38687/05_2025/8xuz_38687.map" model { file = "/net/cci-nas-00/data/ceres_data/8xuz_38687/05_2025/8xuz_38687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xuz_38687/05_2025/8xuz_38687.cif" } resolution = 3.05 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= 0.016 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 122 5.16 5 C 17108 2.51 5 N 4355 2.21 5 O 5240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26825 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6499 Classifications: {'peptide': 836} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 42, 'TRANS': 793} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 6527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6527 Classifications: {'peptide': 839} Link IDs: {'PTRANS': 42, 'TRANS': 796} Chain breaks: 7 Chain: "C" Number of atoms: 8112 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1035, 8105 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 55, 'TRANS': 979} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1035, 8105 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 55, 'TRANS': 979} Chain breaks: 6 bond proxies already assigned to first conformer: 8293 Chain: "L" 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: "D" 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: "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: "I" 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: "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: "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: "M" 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 Chain: "N" 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: "O" 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 19.20, per 1000 atoms: 0.72 Number of scatterers: 26825 At special positions: 0 Unit cell: (139.695, 136.68, 213.06, 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 122 16.00 O 5240 8.00 N 4355 7.00 C 17108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 390 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 141 " distance=2.03 Simple disulfide: pdb=" SG CYS L 344 " - pdb=" SG CYS L 361 " distance=2.03 Simple disulfide: pdb=" SG CYS L 530 " - pdb=" SG CYS L 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " NAG M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 233 " " NAG A1304 " - " ASN A 281 " " NAG A1305 " - " ASN A 614 " " NAG A1306 " - " ASN A 655 " " NAG A1307 " - " ASN A 707 " " NAG A1308 " - " ASN A1072 " " NAG A1309 " - " ASN A1096 " " NAG A1310 " - " ASN A1132 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 233 " " NAG B1304 " - " ASN B 281 " " NAG B1305 " - " ASN B 614 " " NAG B1306 " - " ASN B 655 " " NAG B1307 " - " ASN B 707 " " NAG B1308 " - " ASN B1072 " " NAG B1309 " - " ASN B1096 " " NAG B1310 " - " ASN B1132 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 233 " " NAG C1304 " - " ASN C 281 " " NAG C1305 " - " ASN C 655 " " NAG C1306 " - " ASN C 707 " " NAG C1307 " - " ASN C1072 " " NAG C1308 " - " ASN C1096 " " NAG C1309 " - " ASN C 614 " " NAG C1310 " - " ASN C 353 " " NAG C1311 " - " ASN C 342 " " NAG D 1 " - " ASN A 799 " " NAG F 1 " - " ASN A 715 " " NAG G 1 " - " ASN B 715 " " NAG H 1 " - " ASN L 546 " " NAG I 1 " - " ASN C 165 " " NAG J 1 " - " ASN C 715 " " NAG K 1 " - " ASN C 799 " " NAG N 1 " - " ASN L 90 " " NAG O 1 " - " ASN L 103 " Time building additional restraints: 7.56 Conformation dependent library (CDL) restraints added in 4.6 seconds 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6208 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 41 sheets defined 33.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 614 through 624 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 removed outlier: 3.583A pdb=" N THR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.717A pdb=" N THR A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.575A pdb=" N ALA A 888 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 905 Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.595A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 937 removed outlier: 3.659A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 937 " --> pdb=" O GLN A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.857A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.553A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 614 through 624 Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.076A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.645A pdb=" N ASP B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.544A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.595A pdb=" N GLY B 887 " --> pdb=" O TRP B 884 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 888 " --> pdb=" O THR B 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 884 through 888' Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.724A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.514A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE B 937 " --> pdb=" O GLN B 933 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR B 939 " --> pdb=" O SER B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 removed outlier: 4.003A pdb=" N VAL B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 950 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.602A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 3.911A pdb=" N GLU B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 348 through 352 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.904A pdb=" N TYR C 368 " --> pdb=" O TYR C 364 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 382 through 388 removed outlier: 4.663A pdb=" N ASN C 387 " --> pdb=" O THR C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 4.382A pdb=" N SER C 407 " --> pdb=" O ASN C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.541A pdb=" N TYR C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 624 Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.635A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C 773 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 776 " --> pdb=" O GLN C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 882 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.560A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.639A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 936 " --> pdb=" O ILE C 932 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 937 " --> pdb=" O GLN C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.723A pdb=" N GLN C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 948 " --> pdb=" O GLY C 944 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN C 953 " --> pdb=" O VAL C 949 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C 954 " --> pdb=" O VAL C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.069A pdb=" N GLU C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN C 990 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1116 No H-bonds generated for 'chain 'C' and resid 1114 through 1116' Processing helix chain 'L' and resid 20 through 53 removed outlier: 3.693A pdb=" N LYS L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS L 31 " --> pdb=" O THR L 27 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE L 32 " --> pdb=" O PHE L 28 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N HIS L 34 " --> pdb=" O ASP L 30 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 83 removed outlier: 3.655A pdb=" N THR L 78 " --> pdb=" O LYS L 74 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 104 removed outlier: 3.825A pdb=" N LEU L 100 " --> pdb=" O GLN L 96 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN L 101 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN L 102 " --> pdb=" O GLN L 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY L 104 " --> pdb=" O LEU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 130 removed outlier: 4.032A pdb=" N ARG L 115 " --> pdb=" O ASP L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 154 removed outlier: 3.579A pdb=" N ILE L 151 " --> pdb=" O GLY L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 172 removed outlier: 3.796A pdb=" N GLU L 166 " --> pdb=" O LEU L 162 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG L 169 " --> pdb=" O TRP L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 192 Proline residue: L 178 - end of helix Processing helix chain 'L' and resid 199 through 205 removed outlier: 3.693A pdb=" N TRP L 203 " --> pdb=" O TYR L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 218 through 252 removed outlier: 3.820A pdb=" N ILE L 223 " --> pdb=" O ARG L 219 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU L 224 " --> pdb=" O GLY L 220 " (cutoff:3.500A) Proline residue: L 235 - end of helix removed outlier: 3.715A pdb=" N HIS L 239 " --> pdb=" O PRO L 235 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 282 removed outlier: 3.609A pdb=" N SER L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU L 281 " --> pdb=" O ASN L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 300 removed outlier: 3.779A pdb=" N VAL L 298 " --> pdb=" O THR L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 318 removed outlier: 3.724A pdb=" N PHE L 308 " --> pdb=" O ALA L 304 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA L 311 " --> pdb=" O ILE L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 329 Processing helix chain 'L' and resid 365 through 385 removed outlier: 3.901A pdb=" N TYR L 385 " --> pdb=" O TYR L 381 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 388 No H-bonds generated for 'chain 'L' and resid 386 through 388' Processing helix chain 'L' and resid 389 through 396 removed outlier: 4.352A pdb=" N ASN L 394 " --> pdb=" O LEU L 391 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY L 395 " --> pdb=" O LEU L 392 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA L 396 " --> pdb=" O ARG L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 397 through 413 removed outlier: 3.637A pdb=" N SER L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 422 Processing helix chain 'L' and resid 431 through 447 removed outlier: 3.621A pdb=" N THR L 445 " --> pdb=" O LYS L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 465 Processing helix chain 'L' and resid 472 through 484 removed outlier: 3.581A pdb=" N GLU L 483 " --> pdb=" O GLU L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 502 Processing helix chain 'L' and resid 503 through 508 Processing helix chain 'L' and resid 512 through 534 removed outlier: 3.878A pdb=" N TYR L 516 " --> pdb=" O PHE L 512 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU L 520 " --> pdb=" O TYR L 516 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE L 523 " --> pdb=" O THR L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 561 removed outlier: 3.957A pdb=" N LYS L 553 " --> pdb=" O GLU L 549 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY L 561 " --> pdb=" O MET L 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 562 through 564 No H-bonds generated for 'chain 'L' and resid 562 through 564' Processing helix chain 'L' and resid 565 through 574 Processing helix chain 'L' and resid 581 through 588 Processing helix chain 'L' and resid 588 through 598 removed outlier: 3.963A pdb=" N TRP L 594 " --> pdb=" O PRO L 590 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP L 597 " --> pdb=" O THR L 593 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN L 598 " --> pdb=" O TRP L 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.567A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN A 61 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TYR A 268 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 93 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 267 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 203 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N SER A 205 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N HIS A 207 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N LEU A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL A 36 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 removed outlier: 3.640A pdb=" N LEU A 141 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA A 242 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A 101 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 277 through 278 removed outlier: 6.963A pdb=" N LYS A 277 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 310 through 318 removed outlier: 5.285A pdb=" N ILE A 311 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR A 597 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN A 313 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 595 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 315 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.797A pdb=" N ARG A 327 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 585 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 653 Processing sheet with id=AA8, first strand: chain 'A' and resid 699 through 701 Processing sheet with id=AA9, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.690A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 715 through 720 removed outlier: 3.662A pdb=" N SER A 719 " --> pdb=" O THR A1064 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 715 through 720 removed outlier: 3.662A pdb=" N SER A 719 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.742A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1118 through 1119 Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.557A pdb=" N TYR B 264 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 265 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE B 201 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP B 227 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 203 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N HIS B 207 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N ALA B 221 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 36 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.714A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.269A pdb=" N ASP B 286 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.773A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 107 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 310 through 318 removed outlier: 6.959A pdb=" N VAL B 593 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN B 316 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY B 591 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.043A pdb=" N ILE B 325 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 551 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 652 through 658 removed outlier: 5.418A pdb=" N THR B 694 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B 656 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 689 " --> pdb=" O GLN B 673 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 709 through 726 removed outlier: 6.821A pdb=" N SER B 709 " --> pdb=" O THR B1074 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B1074 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 711 " --> pdb=" O ASN B1072 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN B1072 " --> pdb=" O ALA B 711 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 709 through 726 removed outlier: 6.821A pdb=" N SER B 709 " --> pdb=" O THR B1074 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B1074 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 711 " --> pdb=" O ASN B1072 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN B1072 " --> pdb=" O ALA B 711 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B1074 " --> pdb=" O SER B1095 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.729A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1118 through 1119 Processing sheet with id=AC7, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.770A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 203 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL C 226 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER C 205 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N HIS C 207 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N LEU C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 36 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 48 through 50 removed outlier: 4.181A pdb=" N ASP C 286 " --> pdb=" O LYS C 277 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.508A pdb=" N ASP C 53 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.824A pdb=" N ILE C 105 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 310 through 318 removed outlier: 6.904A pdb=" N VAL C 593 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN C 316 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 591 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.507A pdb=" N VAL C 394 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 390 through 391 Processing sheet with id=AD5, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AD6, first strand: chain 'C' and resid 472 through 473 removed outlier: 3.969A pdb=" N TYR C 472 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR C 487 " --> pdb=" O TYR C 472 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 652 through 653 Processing sheet with id=AD8, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.663A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.780A pdb=" N SER C 719 " --> pdb=" O THR C1064 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C1054 " --> pdb=" O GLY C1057 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.763A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1079 through 1080 Processing sheet with id=AE3, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AE4, first strand: chain 'L' and resid 262 through 263 removed outlier: 5.525A pdb=" N LEU L 262 " --> pdb=" O VAL L 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'L' and resid 347 through 350 1091 hydrogen bonds defined for protein. 3061 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: 10.63 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8472 1.34 - 1.46: 6661 1.46 - 1.58: 12139 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 27442 Sorted by residual: bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 ... (remaining 27437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 36505 1.54 - 3.08: 717 3.08 - 4.63: 77 4.63 - 6.17: 28 6.17 - 7.71: 4 Bond angle restraints: 37331 Sorted by residual: angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 113.10 105.39 7.71 9.70e-01 1.06e+00 6.32e+01 angle pdb=" N PRO A 82 " pdb=" CA PRO A 82 " pdb=" CB PRO A 82 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.55e+01 angle pdb=" C ASN L 437 " pdb=" N PHE L 438 " pdb=" CA PHE L 438 " ideal model delta sigma weight residual 120.68 114.90 5.78 1.70e+00 3.46e-01 1.15e+01 angle pdb=" CA VAL B 130 " pdb=" C VAL B 130 " pdb=" O VAL B 130 " ideal model delta sigma weight residual 119.38 121.63 -2.25 8.70e-01 1.32e+00 6.68e+00 angle pdb=" N GLU L 75 " pdb=" CA GLU L 75 " pdb=" CB GLU L 75 " ideal model delta sigma weight residual 110.28 114.22 -3.94 1.55e+00 4.16e-01 6.46e+00 ... (remaining 37326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 16081 24.76 - 49.52: 844 49.52 - 74.28: 115 74.28 - 99.04: 39 99.04 - 123.80: 16 Dihedral angle restraints: 17095 sinusoidal: 7464 harmonic: 9631 Sorted by residual: dihedral pdb=" CB CYS C 479 " pdb=" SG CYS C 479 " pdb=" SG CYS C 486 " pdb=" CB CYS C 486 " ideal model delta sinusoidal sigma weight residual 93.00 6.13 86.87 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS L 344 " pdb=" SG CYS L 344 " pdb=" SG CYS L 361 " pdb=" CB CYS L 361 " ideal model delta sinusoidal sigma weight residual -86.00 -170.39 84.39 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS L 133 " pdb=" SG CYS L 133 " pdb=" SG CYS L 141 " pdb=" CB CYS L 141 " ideal model delta sinusoidal sigma weight residual 93.00 24.09 68.91 1 1.00e+01 1.00e-02 6.14e+01 ... (remaining 17092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4152 0.096 - 0.192: 228 0.192 - 0.288: 8 0.288 - 0.384: 1 0.384 - 0.479: 1 Chirality restraints: 4390 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 707 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN L 103 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1072 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 4387 not shown) Planarity restraints: 4766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 491 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO L 492 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 492 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 492 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 173 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO B 174 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 293 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 294 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 294 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 294 " 0.022 5.00e-02 4.00e+02 ... (remaining 4763 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 868 2.71 - 3.26: 26178 3.26 - 3.80: 42001 3.80 - 4.35: 51869 4.35 - 4.90: 89262 Nonbonded interactions: 210178 Sorted by model distance: nonbonded pdb=" NH2 ARG L 177 " pdb=" OE1 GLU L 495 " model vdw 2.161 3.120 nonbonded pdb=" OE1 GLU L 375 " pdb=" O4 MAN O 4 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR A 25 " pdb=" O HIS A 66 " model vdw 2.201 3.040 nonbonded pdb=" O ASN C 438 " pdb=" OG SER C 442 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR A 322 " pdb=" OE1 GLU A 323 " model vdw 2.239 3.040 ... (remaining 210173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 67 or resid 82 through 1137 or resid 1301 throu \ gh 1310)) selection = (chain 'B' and (resid 25 through 67 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 826 or resid 850 through 1137 or r \ esid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) } 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=0.00 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: 7.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 66.970 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.150 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 0.081 27534 Z= 0.156 Angle : 0.542 9.914 37573 Z= 0.265 Chirality : 0.044 0.479 4390 Planarity : 0.004 0.046 4725 Dihedral : 15.162 123.797 10785 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: -0.00 (0.15), residues: 3261 helix: 1.90 (0.17), residues: 955 sheet: -0.08 (0.22), residues: 599 loop : -1.12 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 884 HIS 0.011 0.001 HIS L 401 PHE 0.018 0.001 PHE B 904 TYR 0.011 0.001 TYR L 50 ARG 0.003 0.000 ARG L 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 41) link_NAG-ASN : angle 2.14078 ( 123) link_ALPHA1-6 : bond 0.00405 ( 1) link_ALPHA1-6 : angle 1.52025 ( 3) link_BETA1-4 : bond 0.00732 ( 15) link_BETA1-4 : angle 2.25936 ( 45) link_ALPHA1-3 : bond 0.00209 ( 1) link_ALPHA1-3 : angle 1.85897 ( 3) hydrogen bonds : bond 0.20108 ( 1075) hydrogen bonds : angle 7.42633 ( 3061) SS BOND : bond 0.00216 ( 34) SS BOND : angle 0.92798 ( 68) covalent geometry : bond 0.00309 (27442) covalent geometry : angle 0.52197 (37331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TYR cc_start: 0.7687 (m-10) cc_final: 0.7417 (m-80) REVERT: A 617 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8140 (tt0) REVERT: B 127 PHE cc_start: 0.6597 (m-80) cc_final: 0.6368 (m-80) REVERT: B 177 MET cc_start: 0.6474 (pmm) cc_final: 0.5488 (ptm) REVERT: B 227 ASP cc_start: 0.8610 (t0) cc_final: 0.8383 (t0) REVERT: B 582 ILE cc_start: 0.8284 (pt) cc_final: 0.7641 (pt) REVERT: B 630 THR cc_start: 0.7244 (p) cc_final: 0.6935 (p) REVERT: B 900 MET cc_start: 0.8857 (tpp) cc_final: 0.8508 (mmt) REVERT: B 986 GLU cc_start: 0.8092 (mp0) cc_final: 0.7540 (mp0) REVERT: C 41 LYS cc_start: 0.8303 (mttt) cc_final: 0.8023 (mttt) REVERT: C 117 LEU cc_start: 0.7513 (mt) cc_final: 0.7284 (mt) REVERT: C 121 ASN cc_start: 0.5366 (m-40) cc_final: 0.5136 (t0) REVERT: C 427 ASP cc_start: 0.8044 (m-30) cc_final: 0.7565 (p0) REVERT: C 451 TRP cc_start: 0.8228 (m100) cc_final: 0.7596 (m100) REVERT: C 493 TYR cc_start: 0.7579 (p90) cc_final: 0.7314 (p90) REVERT: C 570 THR cc_start: 0.8888 (m) cc_final: 0.8439 (p) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.4060 time to fit residues: 168.4102 Evaluate side-chains 152 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 297 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A 893 GLN B 899 GLN B1003 GLN ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 ASN C 611 GLN C1000 GLN C1104 GLN ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.134555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079696 restraints weight = 91603.096| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 5.01 r_work: 0.2913 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27534 Z= 0.155 Angle : 0.591 10.712 37573 Z= 0.299 Chirality : 0.045 0.414 4390 Planarity : 0.004 0.073 4725 Dihedral : 9.546 112.738 4771 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.69 % Allowed : 5.69 % Favored : 93.62 % 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 (0.15), residues: 3261 helix: 2.16 (0.17), residues: 979 sheet: 0.18 (0.21), residues: 644 loop : -1.25 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.013 0.001 HIS L 401 PHE 0.035 0.002 PHE L 438 TYR 0.018 0.001 TYR B1065 ARG 0.004 0.000 ARG C 993 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 41) link_NAG-ASN : angle 2.15491 ( 123) link_ALPHA1-6 : bond 0.00560 ( 1) link_ALPHA1-6 : angle 2.57061 ( 3) link_BETA1-4 : bond 0.00713 ( 15) link_BETA1-4 : angle 2.18377 ( 45) link_ALPHA1-3 : bond 0.00362 ( 1) link_ALPHA1-3 : angle 2.85342 ( 3) hydrogen bonds : bond 0.06144 ( 1075) hydrogen bonds : angle 5.49337 ( 3061) SS BOND : bond 0.00365 ( 34) SS BOND : angle 1.17155 ( 68) covalent geometry : bond 0.00357 (27442) covalent geometry : angle 0.57179 (37331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8373 (m-80) cc_final: 0.8160 (m-80) REVERT: A 170 TYR cc_start: 0.6876 (t80) cc_final: 0.6644 (t80) REVERT: A 617 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8508 (tt0) REVERT: A 983 ASP cc_start: 0.7802 (p0) cc_final: 0.7418 (p0) REVERT: B 177 MET cc_start: 0.6366 (pmm) cc_final: 0.5838 (ptm) REVERT: B 582 ILE cc_start: 0.8751 (pt) cc_final: 0.8483 (pt) REVERT: B 628 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7416 (p) REVERT: B 630 THR cc_start: 0.7415 (p) cc_final: 0.7097 (p) REVERT: C 41 LYS cc_start: 0.8355 (mttt) cc_final: 0.8061 (mttm) REVERT: C 427 ASP cc_start: 0.8034 (m-30) cc_final: 0.7499 (p0) REVERT: C 451 TRP cc_start: 0.8424 (m100) cc_final: 0.7815 (m100) REVERT: C 493 TYR cc_start: 0.7597 (p90) cc_final: 0.7353 (p90) REVERT: C 514 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 570 THR cc_start: 0.9031 (m) cc_final: 0.8641 (p) REVERT: L 190 MET cc_start: 0.7854 (tpt) cc_final: 0.7582 (tpt) REVERT: L 270 MET cc_start: 0.3579 (ttm) cc_final: 0.3285 (ttm) outliers start: 20 outliers final: 13 residues processed: 177 average time/residue: 0.3758 time to fit residues: 109.3302 Evaluate side-chains 152 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 485 ASN Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1036 LYS Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 421 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 158 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 241 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 322 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN C1104 GLN ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.137492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.082868 restraints weight = 93494.743| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.44 r_work: 0.2888 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27534 Z= 0.189 Angle : 0.594 12.312 37573 Z= 0.299 Chirality : 0.046 0.409 4390 Planarity : 0.004 0.068 4725 Dihedral : 8.732 108.541 4771 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.59 % Allowed : 8.45 % Favored : 90.97 % 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: 0.08 (0.15), residues: 3261 helix: 2.16 (0.17), residues: 982 sheet: 0.08 (0.21), residues: 651 loop : -1.34 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 435 HIS 0.010 0.001 HIS L 401 PHE 0.030 0.002 PHE L 438 TYR 0.019 0.001 TYR B1065 ARG 0.006 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 41) link_NAG-ASN : angle 2.21555 ( 123) link_ALPHA1-6 : bond 0.01024 ( 1) link_ALPHA1-6 : angle 2.97782 ( 3) link_BETA1-4 : bond 0.00630 ( 15) link_BETA1-4 : angle 2.18959 ( 45) link_ALPHA1-3 : bond 0.00786 ( 1) link_ALPHA1-3 : angle 2.19010 ( 3) hydrogen bonds : bond 0.06301 ( 1075) hydrogen bonds : angle 5.23794 ( 3061) SS BOND : bond 0.00280 ( 34) SS BOND : angle 1.24277 ( 68) covalent geometry : bond 0.00453 (27442) covalent geometry : angle 0.57355 (37331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TYR cc_start: 0.8140 (m-10) cc_final: 0.7700 (m-80) REVERT: B 628 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.7279 (p) REVERT: B 630 THR cc_start: 0.7391 (p) cc_final: 0.7044 (p) REVERT: C 41 LYS cc_start: 0.8390 (mttt) cc_final: 0.8120 (mttm) REVERT: C 170 TYR cc_start: 0.8176 (t80) cc_final: 0.7826 (t80) REVERT: C 236 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7698 (mtp-110) REVERT: C 427 ASP cc_start: 0.8061 (m-30) cc_final: 0.7555 (p0) REVERT: C 451 TRP cc_start: 0.8422 (m100) cc_final: 0.7900 (m100) REVERT: C 493 TYR cc_start: 0.7480 (p90) cc_final: 0.7159 (p90) REVERT: C 514 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7366 (tm-30) REVERT: C 570 THR cc_start: 0.8986 (m) cc_final: 0.8535 (p) REVERT: L 270 MET cc_start: 0.4138 (ttm) cc_final: 0.3527 (ttm) outliers start: 17 outliers final: 14 residues processed: 159 average time/residue: 0.3644 time to fit residues: 95.4312 Evaluate side-chains 150 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1036 LYS Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain L residue 421 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 262 optimal weight: 0.9990 chunk 309 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 chunk 292 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C1000 GLN C1104 GLN L 61 ASN ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.136962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.082332 restraints weight = 86612.945| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.76 r_work: 0.2940 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27534 Z= 0.131 Angle : 0.560 12.799 37573 Z= 0.281 Chirality : 0.044 0.388 4390 Planarity : 0.004 0.067 4725 Dihedral : 8.039 103.320 4771 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.97 % Allowed : 9.45 % Favored : 89.59 % 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: 0.15 (0.15), residues: 3261 helix: 2.23 (0.17), residues: 980 sheet: 0.14 (0.21), residues: 652 loop : -1.31 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 478 HIS 0.009 0.001 HIS L 401 PHE 0.026 0.001 PHE L 438 TYR 0.016 0.001 TYR B1065 ARG 0.006 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 41) link_NAG-ASN : angle 2.14842 ( 123) link_ALPHA1-6 : bond 0.00847 ( 1) link_ALPHA1-6 : angle 2.58234 ( 3) link_BETA1-4 : bond 0.00693 ( 15) link_BETA1-4 : angle 2.09444 ( 45) link_ALPHA1-3 : bond 0.00887 ( 1) link_ALPHA1-3 : angle 2.17177 ( 3) hydrogen bonds : bond 0.05555 ( 1075) hydrogen bonds : angle 5.00909 ( 3061) SS BOND : bond 0.00209 ( 34) SS BOND : angle 1.33953 ( 68) covalent geometry : bond 0.00296 (27442) covalent geometry : angle 0.53950 (37331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TYR cc_start: 0.8027 (m-10) cc_final: 0.7551 (m-80) REVERT: B 177 MET cc_start: 0.5845 (pmm) cc_final: 0.4894 (ptm) REVERT: B 630 THR cc_start: 0.7333 (p) cc_final: 0.7042 (p) REVERT: C 41 LYS cc_start: 0.8272 (mttt) cc_final: 0.7979 (mttm) REVERT: C 170 TYR cc_start: 0.8226 (t80) cc_final: 0.7867 (t80) REVERT: C 200 TYR cc_start: 0.9155 (m-80) cc_final: 0.8534 (t80) REVERT: C 236 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7641 (mtp-110) REVERT: C 420 TYR cc_start: 0.8015 (m-80) cc_final: 0.7676 (m-80) REVERT: C 427 ASP cc_start: 0.8007 (m-30) cc_final: 0.7504 (p0) REVERT: C 451 TRP cc_start: 0.8369 (m100) cc_final: 0.7824 (m100) REVERT: C 493 TYR cc_start: 0.7476 (p90) cc_final: 0.7197 (p90) REVERT: C 514 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7346 (tm-30) REVERT: C 570 THR cc_start: 0.8945 (m) cc_final: 0.8521 (p) REVERT: L 270 MET cc_start: 0.4157 (ttm) cc_final: 0.3516 (ttm) outliers start: 28 outliers final: 15 residues processed: 162 average time/residue: 0.3617 time to fit residues: 96.9003 Evaluate side-chains 150 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 283 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 53 optimal weight: 0.8980 chunk 323 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 313 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 GLN A 639 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 ASN C1000 GLN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.137160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.082718 restraints weight = 76920.331| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.55 r_work: 0.2941 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27534 Z= 0.147 Angle : 0.568 14.663 37573 Z= 0.284 Chirality : 0.045 0.391 4390 Planarity : 0.004 0.066 4725 Dihedral : 7.622 101.306 4771 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 0.93 % Allowed : 10.66 % Favored : 88.41 % 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: 0.12 (0.15), residues: 3261 helix: 2.18 (0.17), residues: 989 sheet: 0.11 (0.21), residues: 653 loop : -1.33 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 884 HIS 0.009 0.001 HIS L 401 PHE 0.024 0.001 PHE L 438 TYR 0.017 0.001 TYR B1065 ARG 0.007 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 41) link_NAG-ASN : angle 2.17049 ( 123) link_ALPHA1-6 : bond 0.00937 ( 1) link_ALPHA1-6 : angle 2.58684 ( 3) link_BETA1-4 : bond 0.00704 ( 15) link_BETA1-4 : angle 2.07086 ( 45) link_ALPHA1-3 : bond 0.00996 ( 1) link_ALPHA1-3 : angle 2.17516 ( 3) hydrogen bonds : bond 0.05632 ( 1075) hydrogen bonds : angle 4.91963 ( 3061) SS BOND : bond 0.00215 ( 34) SS BOND : angle 1.29994 ( 68) covalent geometry : bond 0.00345 (27442) covalent geometry : angle 0.54728 (37331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6013 (pmm) cc_final: 0.4703 (ppp) REVERT: B 227 ASP cc_start: 0.8757 (t0) cc_final: 0.8556 (t0) REVERT: B 630 THR cc_start: 0.7381 (p) cc_final: 0.7077 (p) REVERT: C 41 LYS cc_start: 0.8337 (mttt) cc_final: 0.8088 (mttm) REVERT: C 170 TYR cc_start: 0.8199 (t80) cc_final: 0.7818 (t80) REVERT: C 420 TYR cc_start: 0.8000 (m-80) cc_final: 0.7757 (m-80) REVERT: C 427 ASP cc_start: 0.8008 (m-30) cc_final: 0.7498 (p0) REVERT: C 451 TRP cc_start: 0.8381 (m100) cc_final: 0.7873 (m100) REVERT: C 459 LYS cc_start: 0.8136 (tppt) cc_final: 0.7403 (tppt) REVERT: C 493 TYR cc_start: 0.7206 (p90) cc_final: 0.6927 (p90) REVERT: C 514 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7296 (tm-30) REVERT: C 570 THR cc_start: 0.8958 (m) cc_final: 0.8528 (p) REVERT: C 626 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8562 (mm-40) outliers start: 27 outliers final: 19 residues processed: 158 average time/residue: 0.3694 time to fit residues: 96.9607 Evaluate side-chains 152 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 421 ILE Chi-restraints excluded: chain L residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 105 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 68 optimal weight: 0.0010 chunk 88 optimal weight: 5.9990 chunk 275 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 GLN A 639 ASN A1133 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN C 330 ASN C1104 GLN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.134665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080059 restraints weight = 86967.473| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 4.30 r_work: 0.2870 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 27534 Z= 0.227 Angle : 0.624 14.763 37573 Z= 0.314 Chirality : 0.047 0.430 4390 Planarity : 0.004 0.069 4725 Dihedral : 7.405 102.874 4771 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.07 % Allowed : 11.52 % Favored : 87.41 % 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: -0.11 (0.15), residues: 3261 helix: 1.99 (0.17), residues: 998 sheet: -0.11 (0.21), residues: 620 loop : -1.43 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 884 HIS 0.008 0.001 HIS L 401 PHE 0.037 0.002 PHE C 904 TYR 0.029 0.002 TYR C 452 ARG 0.008 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 41) link_NAG-ASN : angle 2.33908 ( 123) link_ALPHA1-6 : bond 0.00584 ( 1) link_ALPHA1-6 : angle 2.16903 ( 3) link_BETA1-4 : bond 0.00651 ( 15) link_BETA1-4 : angle 2.15501 ( 45) link_ALPHA1-3 : bond 0.00835 ( 1) link_ALPHA1-3 : angle 2.46108 ( 3) hydrogen bonds : bond 0.06617 ( 1075) hydrogen bonds : angle 5.05543 ( 3061) SS BOND : bond 0.00310 ( 34) SS BOND : angle 1.59850 ( 68) covalent geometry : bond 0.00552 (27442) covalent geometry : angle 0.60234 (37331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6055 (pmm) cc_final: 0.4941 (ptm) REVERT: B 630 THR cc_start: 0.7393 (p) cc_final: 0.7094 (p) REVERT: C 41 LYS cc_start: 0.8489 (mttt) cc_final: 0.8256 (mttm) REVERT: C 170 TYR cc_start: 0.8207 (t80) cc_final: 0.7801 (t80) REVERT: C 236 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7538 (mtp-110) REVERT: C 427 ASP cc_start: 0.8060 (m-30) cc_final: 0.7540 (p0) REVERT: C 451 TRP cc_start: 0.8406 (m100) cc_final: 0.7872 (m100) REVERT: C 459 LYS cc_start: 0.8037 (tppt) cc_final: 0.7490 (tppt) REVERT: C 493 TYR cc_start: 0.7347 (p90) cc_final: 0.6990 (p90) REVERT: C 514 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7328 (tm-30) REVERT: C 570 THR cc_start: 0.8978 (m) cc_final: 0.8505 (p) REVERT: C 626 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8427 (mm-40) REVERT: L 270 MET cc_start: 0.3194 (mmt) cc_final: 0.1996 (tpp) outliers start: 31 outliers final: 22 residues processed: 157 average time/residue: 0.3621 time to fit residues: 95.0989 Evaluate side-chains 149 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1036 LYS Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 491 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 305 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 320 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.133710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.078326 restraints weight = 93410.965| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 4.97 r_work: 0.2893 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27534 Z= 0.156 Angle : 0.583 14.839 37573 Z= 0.290 Chirality : 0.045 0.407 4390 Planarity : 0.004 0.069 4725 Dihedral : 7.119 102.405 4771 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 0.97 % Allowed : 12.52 % Favored : 86.52 % 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: -0.01 (0.15), residues: 3261 helix: 2.10 (0.17), residues: 995 sheet: -0.03 (0.21), residues: 649 loop : -1.41 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 884 HIS 0.008 0.001 HIS L 401 PHE 0.022 0.001 PHE C 937 TYR 0.025 0.001 TYR C 452 ARG 0.006 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 41) link_NAG-ASN : angle 2.26648 ( 123) link_ALPHA1-6 : bond 0.00534 ( 1) link_ALPHA1-6 : angle 1.63485 ( 3) link_BETA1-4 : bond 0.00685 ( 15) link_BETA1-4 : angle 2.03916 ( 45) link_ALPHA1-3 : bond 0.00854 ( 1) link_ALPHA1-3 : angle 2.09259 ( 3) hydrogen bonds : bond 0.05781 ( 1075) hydrogen bonds : angle 4.87675 ( 3061) SS BOND : bond 0.00269 ( 34) SS BOND : angle 1.66102 ( 68) covalent geometry : bond 0.00369 (27442) covalent geometry : angle 0.56064 (37331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6083 (pmm) cc_final: 0.4606 (ppp) REVERT: B 630 THR cc_start: 0.7340 (p) cc_final: 0.7128 (p) REVERT: B 688 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: C 41 LYS cc_start: 0.8350 (mttt) cc_final: 0.8079 (mttt) REVERT: C 170 TYR cc_start: 0.8084 (t80) cc_final: 0.7688 (t80) REVERT: C 200 TYR cc_start: 0.9089 (m-80) cc_final: 0.8487 (t80) REVERT: C 236 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7573 (mtp85) REVERT: C 427 ASP cc_start: 0.8072 (m-30) cc_final: 0.7571 (p0) REVERT: C 451 TRP cc_start: 0.8432 (m100) cc_final: 0.7909 (m100) REVERT: C 459 LYS cc_start: 0.8076 (tppt) cc_final: 0.7719 (tppt) REVERT: C 493 TYR cc_start: 0.7339 (p90) cc_final: 0.6984 (p90) REVERT: C 514 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7344 (tm-30) REVERT: C 570 THR cc_start: 0.8896 (m) cc_final: 0.8458 (p) REVERT: C 626 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8398 (mm-40) REVERT: L 270 MET cc_start: 0.3297 (mmt) cc_final: 0.2160 (tpp) outliers start: 28 outliers final: 26 residues processed: 152 average time/residue: 0.3730 time to fit residues: 94.1249 Evaluate side-chains 154 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1036 LYS Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 274 PHE Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 66 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 277 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS C 330 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 61 ASN ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.130654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074551 restraints weight = 82098.150| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.88 r_work: 0.2921 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27534 Z= 0.171 Angle : 0.590 13.226 37573 Z= 0.294 Chirality : 0.045 0.429 4390 Planarity : 0.004 0.071 4725 Dihedral : 7.025 102.527 4771 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 1.14 % Allowed : 12.62 % Favored : 86.24 % 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: -0.05 (0.15), residues: 3261 helix: 2.08 (0.17), residues: 995 sheet: -0.07 (0.21), residues: 624 loop : -1.41 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 884 HIS 0.008 0.001 HIS L 401 PHE 0.025 0.001 PHE C 904 TYR 0.026 0.001 TYR C 452 ARG 0.006 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 41) link_NAG-ASN : angle 2.46567 ( 123) link_ALPHA1-6 : bond 0.00314 ( 1) link_ALPHA1-6 : angle 1.55823 ( 3) link_BETA1-4 : bond 0.00659 ( 15) link_BETA1-4 : angle 2.04118 ( 45) link_ALPHA1-3 : bond 0.00822 ( 1) link_ALPHA1-3 : angle 2.05126 ( 3) hydrogen bonds : bond 0.05922 ( 1075) hydrogen bonds : angle 4.87349 ( 3061) SS BOND : bond 0.00255 ( 34) SS BOND : angle 1.60369 ( 68) covalent geometry : bond 0.00407 (27442) covalent geometry : angle 0.56535 (37331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6060 (pmm) cc_final: 0.4521 (ppp) REVERT: B 630 THR cc_start: 0.7315 (p) cc_final: 0.7059 (p) REVERT: B 688 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: C 41 LYS cc_start: 0.8386 (mttt) cc_final: 0.8131 (mttt) REVERT: C 200 TYR cc_start: 0.9103 (m-80) cc_final: 0.8513 (t80) REVERT: C 236 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7455 (mtp-110) REVERT: C 318 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.7642 (mtp-110) REVERT: C 427 ASP cc_start: 0.8019 (m-30) cc_final: 0.7513 (p0) REVERT: C 451 TRP cc_start: 0.8375 (m100) cc_final: 0.7857 (m100) REVERT: C 459 LYS cc_start: 0.8217 (tppt) cc_final: 0.7895 (tppt) REVERT: C 493 TYR cc_start: 0.7257 (p90) cc_final: 0.6886 (p90) REVERT: C 514 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 570 THR cc_start: 0.8985 (m) cc_final: 0.8560 (p) REVERT: C 626 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8369 (mm-40) REVERT: L 270 MET cc_start: 0.2967 (mmt) cc_final: 0.1862 (tpp) REVERT: L 516 TYR cc_start: 0.8536 (t80) cc_final: 0.8051 (m-80) outliers start: 33 outliers final: 26 residues processed: 159 average time/residue: 0.3668 time to fit residues: 97.4723 Evaluate side-chains 154 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1102 VAL Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain C residue 1036 LYS Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 274 PHE Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 491 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 37 optimal weight: 0.9980 chunk 292 optimal weight: 0.9990 chunk 175 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.0670 chunk 233 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 239 optimal weight: 0.5980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.132652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078192 restraints weight = 95324.261| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.84 r_work: 0.2933 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27534 Z= 0.106 Angle : 0.564 17.871 37573 Z= 0.277 Chirality : 0.045 0.653 4390 Planarity : 0.004 0.071 4725 Dihedral : 7.383 113.666 4771 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 0.76 % Allowed : 13.03 % Favored : 86.21 % 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: 0.13 (0.15), residues: 3261 helix: 2.22 (0.17), residues: 980 sheet: 0.16 (0.21), residues: 653 loop : -1.34 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 884 HIS 0.008 0.001 HIS L 401 PHE 0.030 0.001 PHE B1073 TYR 0.026 0.001 TYR C 452 ARG 0.006 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 41) link_NAG-ASN : angle 2.09587 ( 123) link_ALPHA1-6 : bond 0.00452 ( 1) link_ALPHA1-6 : angle 1.58279 ( 3) link_BETA1-4 : bond 0.00694 ( 15) link_BETA1-4 : angle 1.93836 ( 45) link_ALPHA1-3 : bond 0.00814 ( 1) link_ALPHA1-3 : angle 1.88540 ( 3) hydrogen bonds : bond 0.04982 ( 1075) hydrogen bonds : angle 4.72510 ( 3061) SS BOND : bond 0.00204 ( 34) SS BOND : angle 1.40721 ( 68) covalent geometry : bond 0.00226 (27442) covalent geometry : angle 0.54506 (37331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.5973 (pmm) cc_final: 0.4344 (ppp) REVERT: C 41 LYS cc_start: 0.8244 (mttt) cc_final: 0.7940 (mttt) REVERT: C 170 TYR cc_start: 0.7971 (t80) cc_final: 0.7683 (t80) REVERT: C 200 TYR cc_start: 0.8987 (m-80) cc_final: 0.8424 (t80) REVERT: C 236 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7425 (mtp-110) REVERT: C 427 ASP cc_start: 0.8058 (m-30) cc_final: 0.7551 (p0) REVERT: C 451 TRP cc_start: 0.8444 (m100) cc_final: 0.7937 (m100) REVERT: C 459 LYS cc_start: 0.8212 (tppt) cc_final: 0.7873 (tppt) REVERT: C 493 TYR cc_start: 0.7243 (p90) cc_final: 0.6857 (p90) REVERT: C 514 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7398 (tm-30) REVERT: C 570 THR cc_start: 0.8889 (m) cc_final: 0.8458 (p) REVERT: C 626 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8352 (mm-40) REVERT: L 270 MET cc_start: 0.2872 (mmt) cc_final: 0.1873 (tpp) REVERT: L 297 MET cc_start: 0.3126 (mtp) cc_final: 0.1633 (ppp) REVERT: L 516 TYR cc_start: 0.8316 (t80) cc_final: 0.7815 (m-80) outliers start: 22 outliers final: 18 residues processed: 148 average time/residue: 0.3806 time to fit residues: 93.9816 Evaluate side-chains 146 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 267 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 240 optimal weight: 0.8980 chunk 321 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 86 optimal weight: 0.0170 chunk 177 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 ASN ** L 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.132510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.077387 restraints weight = 103390.449| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 5.07 r_work: 0.2924 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27534 Z= 0.106 Angle : 0.561 17.993 37573 Z= 0.275 Chirality : 0.044 0.523 4390 Planarity : 0.004 0.069 4725 Dihedral : 7.347 107.879 4771 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 0.69 % Allowed : 13.07 % Favored : 86.24 % 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 (0.15), residues: 3261 helix: 2.28 (0.17), residues: 978 sheet: 0.19 (0.21), residues: 635 loop : -1.28 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 631 HIS 0.012 0.001 HIS L 401 PHE 0.023 0.001 PHE C 215 TYR 0.026 0.001 TYR C 452 ARG 0.005 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 41) link_NAG-ASN : angle 2.21881 ( 123) link_ALPHA1-6 : bond 0.00476 ( 1) link_ALPHA1-6 : angle 1.59717 ( 3) link_BETA1-4 : bond 0.00684 ( 15) link_BETA1-4 : angle 1.90014 ( 45) link_ALPHA1-3 : bond 0.00711 ( 1) link_ALPHA1-3 : angle 1.77676 ( 3) hydrogen bonds : bond 0.04767 ( 1075) hydrogen bonds : angle 4.61869 ( 3061) SS BOND : bond 0.00198 ( 34) SS BOND : angle 1.38546 ( 68) covalent geometry : bond 0.00227 (27442) covalent geometry : angle 0.54064 (37331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6041 (pmm) cc_final: 0.4644 (ppp) REVERT: C 41 LYS cc_start: 0.8286 (mttt) cc_final: 0.7947 (mttm) REVERT: C 170 TYR cc_start: 0.8195 (t80) cc_final: 0.7895 (t80) REVERT: C 200 TYR cc_start: 0.8958 (m-80) cc_final: 0.8450 (t80) REVERT: C 236 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7444 (mtp-110) REVERT: C 413 GLN cc_start: 0.8614 (tt0) cc_final: 0.8385 (tt0) REVERT: C 427 ASP cc_start: 0.8075 (m-30) cc_final: 0.7563 (p0) REVERT: C 451 TRP cc_start: 0.8439 (m100) cc_final: 0.7949 (m100) REVERT: C 459 LYS cc_start: 0.8226 (tppt) cc_final: 0.7950 (tppt) REVERT: C 493 TYR cc_start: 0.7252 (p90) cc_final: 0.6854 (p90) REVERT: C 514 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 570 THR cc_start: 0.8825 (m) cc_final: 0.8392 (p) REVERT: C 626 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8337 (mm-40) REVERT: L 270 MET cc_start: 0.3222 (mmt) cc_final: 0.1839 (tpp) REVERT: L 297 MET cc_start: 0.3222 (mtp) cc_final: 0.1750 (ppp) REVERT: L 480 MET cc_start: 0.6462 (mmt) cc_final: 0.6219 (mpp) outliers start: 20 outliers final: 17 residues processed: 151 average time/residue: 0.3639 time to fit residues: 92.1944 Evaluate side-chains 147 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1134 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 933 GLN Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 257 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 295 optimal weight: 0.0000 chunk 26 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.138489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084901 restraints weight = 88909.085| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.74 r_work: 0.2901 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27534 Z= 0.111 Angle : 0.562 20.841 37573 Z= 0.275 Chirality : 0.044 0.423 4390 Planarity : 0.004 0.085 4725 Dihedral : 7.170 109.096 4771 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 0.62 % Allowed : 13.38 % Favored : 86.00 % 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: 0.23 (0.15), residues: 3261 helix: 2.28 (0.17), residues: 980 sheet: 0.23 (0.21), residues: 637 loop : -1.27 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 631 HIS 0.013 0.001 HIS L 401 PHE 0.020 0.001 PHE C 937 TYR 0.027 0.001 TYR C 452 ARG 0.005 0.000 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 41) link_NAG-ASN : angle 2.07485 ( 123) link_ALPHA1-6 : bond 0.00427 ( 1) link_ALPHA1-6 : angle 1.58965 ( 3) link_BETA1-4 : bond 0.00674 ( 15) link_BETA1-4 : angle 1.89822 ( 45) link_ALPHA1-3 : bond 0.00753 ( 1) link_ALPHA1-3 : angle 1.73151 ( 3) hydrogen bonds : bond 0.04801 ( 1075) hydrogen bonds : angle 4.58756 ( 3061) SS BOND : bond 0.00207 ( 34) SS BOND : angle 1.31681 ( 68) covalent geometry : bond 0.00245 (27442) covalent geometry : angle 0.54431 (37331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18989.91 seconds wall clock time: 327 minutes 30.43 seconds (19650.43 seconds total)