Starting phenix.real_space_refine on Mon Aug 25 22:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xuz_38687/08_2025/8xuz_38687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xuz_38687/08_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_38687/08_2025/8xuz_38687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xuz_38687/08_2025/8xuz_38687.map" model { file = "/net/cci-nas-00/data/ceres_data/8xuz_38687/08_2025/8xuz_38687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xuz_38687/08_2025/8xuz_38687.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.67, per 1000 atoms: 0.29 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: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.00 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: 6.58 Time building geometry restraints manager: 3.35 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 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 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.980 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG L 306 TYR 0.011 0.001 TYR L 50 PHE 0.018 0.001 PHE B 904 TRP 0.010 0.001 TRP A 884 HIS 0.011 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00309 (27442) covalent geometry : angle 0.52197 (37331) SS BOND : bond 0.00216 ( 34) SS BOND : angle 0.92798 ( 68) hydrogen bonds : bond 0.20108 ( 1075) hydrogen bonds : angle 7.42633 ( 3061) link_ALPHA1-3 : bond 0.00209 ( 1) link_ALPHA1-3 : angle 1.85897 ( 3) 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_NAG-ASN : bond 0.00413 ( 41) link_NAG-ASN : angle 2.14078 ( 123) *********************** 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 : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8171 (m-80) cc_final: 0.7845 (m-80) 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: 0.5487 (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: 0.6934 (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: 0.7205 (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: 0.1992 time to fit residues: 82.8898 Evaluate side-chains 151 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 893 GLN A1133 ASN B 899 GLN B1003 GLN ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 ASN C 611 GLN C1000 GLN ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.133705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.080019 restraints weight = 77378.708| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 4.78 r_work: 0.2896 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 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 = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 27534 Z= 0.250 Angle : 0.656 10.678 37573 Z= 0.334 Chirality : 0.048 0.446 4390 Planarity : 0.005 0.072 4725 Dihedral : 9.642 112.695 4771 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.72 % Allowed : 6.28 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.15), residues: 3261 helix: 1.97 (0.17), residues: 981 sheet: -0.00 (0.21), residues: 640 loop : -1.40 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1037 TYR 0.021 0.002 TYR B1065 PHE 0.037 0.002 PHE C 904 TRP 0.014 0.002 TRP C 64 HIS 0.013 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00608 (27442) covalent geometry : angle 0.63571 (37331) SS BOND : bond 0.00322 ( 34) SS BOND : angle 1.35507 ( 68) hydrogen bonds : bond 0.06921 ( 1075) hydrogen bonds : angle 5.53008 ( 3061) link_ALPHA1-3 : bond 0.00364 ( 1) link_ALPHA1-3 : angle 2.84159 ( 3) link_ALPHA1-6 : bond 0.00385 ( 1) link_ALPHA1-6 : angle 2.78622 ( 3) link_BETA1-4 : bond 0.00621 ( 15) link_BETA1-4 : angle 2.30757 ( 45) link_NAG-ASN : bond 0.00427 ( 41) link_NAG-ASN : angle 2.32116 ( 123) *********************** 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 177 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8505 (tt0) REVERT: B 177 MET cc_start: 0.6316 (pmm) cc_final: 0.5960 (ptm) REVERT: B 628 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7524 (p) REVERT: B 630 THR cc_start: 0.7516 (p) cc_final: 0.7132 (p) REVERT: C 41 LYS cc_start: 0.8374 (mttt) cc_final: 0.8126 (mttm) REVERT: C 427 ASP cc_start: 0.8076 (m-30) cc_final: 0.7572 (p0) REVERT: C 451 TRP cc_start: 0.8370 (m100) cc_final: 0.7746 (m100) REVERT: C 514 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 570 THR cc_start: 0.8986 (m) cc_final: 0.8543 (p) REVERT: L 240 LEU cc_start: 0.8321 (mt) cc_final: 0.7775 (pp) REVERT: L 270 MET cc_start: 0.3836 (ttm) cc_final: 0.3607 (ttm) outliers start: 21 outliers final: 15 residues processed: 168 average time/residue: 0.1848 time to fit residues: 50.4230 Evaluate side-chains 154 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 439 LYS Chi-restraints excluded: chain C residue 459 LYS 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 163 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 266 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 301 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.133516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.078670 restraints weight = 92972.161| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 4.95 r_work: 0.2909 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 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 = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27534 Z= 0.123 Angle : 0.558 10.372 37573 Z= 0.280 Chirality : 0.044 0.391 4390 Planarity : 0.004 0.068 4725 Dihedral : 8.612 108.100 4771 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.62 % Allowed : 8.28 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 3261 helix: 2.17 (0.17), residues: 985 sheet: 0.15 (0.21), residues: 655 loop : -1.32 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 318 TYR 0.016 0.001 TYR B1065 PHE 0.029 0.001 PHE L 438 TRP 0.011 0.001 TRP C 435 HIS 0.010 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00267 (27442) covalent geometry : angle 0.53827 (37331) SS BOND : bond 0.00375 ( 34) SS BOND : angle 1.11929 ( 68) hydrogen bonds : bond 0.05605 ( 1075) hydrogen bonds : angle 5.11221 ( 3061) link_ALPHA1-3 : bond 0.00806 ( 1) link_ALPHA1-3 : angle 2.14344 ( 3) link_ALPHA1-6 : bond 0.00863 ( 1) link_ALPHA1-6 : angle 2.57131 ( 3) link_BETA1-4 : bond 0.00770 ( 15) link_BETA1-4 : angle 2.15416 ( 45) link_NAG-ASN : bond 0.00416 ( 41) link_NAG-ASN : angle 2.16181 ( 123) *********************** 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 176 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 1.021 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: A 268 TYR cc_start: 0.8134 (m-10) cc_final: 0.7701 (m-80) REVERT: A 617 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8438 (tt0) REVERT: B 200 TYR cc_start: 0.8377 (m-80) cc_final: 0.7794 (m-80) REVERT: B 628 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7235 (p) REVERT: B 630 THR cc_start: 0.7390 (p) cc_final: 0.7082 (p) REVERT: C 41 LYS cc_start: 0.8331 (mttt) cc_final: 0.8036 (mttm) REVERT: C 170 TYR cc_start: 0.8122 (t80) cc_final: 0.7746 (t80) REVERT: C 236 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7711 (mtp-110) REVERT: C 427 ASP cc_start: 0.8062 (m-30) cc_final: 0.7558 (p0) REVERT: C 451 TRP cc_start: 0.8378 (m100) cc_final: 0.7917 (m100) REVERT: C 514 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7345 (tm-30) REVERT: C 570 THR cc_start: 0.8969 (m) cc_final: 0.8559 (p) REVERT: L 240 LEU cc_start: 0.8214 (mt) cc_final: 0.7699 (pp) REVERT: L 270 MET cc_start: 0.4115 (ttm) cc_final: 0.3397 (ttm) outliers start: 18 outliers final: 14 residues processed: 170 average time/residue: 0.1783 time to fit residues: 49.9579 Evaluate side-chains 153 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 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 421 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 63 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 300 optimal weight: 0.1980 chunk 138 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 284 optimal weight: 20.0000 chunk 305 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 485 ASN C1000 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 = 0.4115 r_free = 0.4115 target = 0.140293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087141 restraints weight = 93662.500| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.71 r_work: 0.2948 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1671 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= 0.117 Angle : 0.554 14.099 37573 Z= 0.276 Chirality : 0.044 0.380 4390 Planarity : 0.004 0.066 4725 Dihedral : 7.910 102.171 4771 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.93 % Allowed : 9.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3261 helix: 2.22 (0.17), residues: 987 sheet: 0.26 (0.21), residues: 655 loop : -1.33 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 318 TYR 0.016 0.001 TYR L 516 PHE 0.027 0.001 PHE L 438 TRP 0.009 0.001 TRP C 435 HIS 0.009 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00257 (27442) covalent geometry : angle 0.53300 (37331) SS BOND : bond 0.00477 ( 34) SS BOND : angle 1.39262 ( 68) hydrogen bonds : bond 0.05208 ( 1075) hydrogen bonds : angle 4.93424 ( 3061) link_ALPHA1-3 : bond 0.00875 ( 1) link_ALPHA1-3 : angle 2.23004 ( 3) link_ALPHA1-6 : bond 0.00902 ( 1) link_ALPHA1-6 : angle 2.49887 ( 3) link_BETA1-4 : bond 0.00697 ( 15) link_BETA1-4 : angle 2.06020 ( 45) link_NAG-ASN : bond 0.00401 ( 41) link_NAG-ASN : angle 2.11407 ( 123) *********************** 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 172 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.080 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: B 177 MET cc_start: 0.6379 (pmm) cc_final: 0.5528 (ptm) REVERT: B 630 THR cc_start: 0.7305 (p) cc_final: 0.7025 (p) REVERT: C 41 LYS cc_start: 0.8271 (mttt) cc_final: 0.7967 (mttm) REVERT: C 170 TYR cc_start: 0.8037 (t80) cc_final: 0.7608 (t80) REVERT: C 236 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7605 (mtp-110) REVERT: C 427 ASP cc_start: 0.8074 (m-30) cc_final: 0.7588 (p0) REVERT: C 451 TRP cc_start: 0.8397 (m100) cc_final: 0.7902 (m100) REVERT: C 514 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7326 (tm-30) REVERT: C 570 THR cc_start: 0.8929 (m) cc_final: 0.8511 (p) REVERT: L 455 MET cc_start: 0.8305 (ppp) cc_final: 0.8105 (tmm) outliers start: 27 outliers final: 14 residues processed: 164 average time/residue: 0.1698 time to fit residues: 46.5990 Evaluate side-chains 151 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 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 323 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 128 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 310 optimal weight: 30.0000 chunk 150 optimal weight: 0.1980 chunk 295 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 78 optimal weight: 0.0070 chunk 209 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.132267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076243 restraints weight = 92656.138| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 4.14 r_work: 0.2928 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 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 = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27534 Z= 0.137 Angle : 0.566 17.093 37573 Z= 0.281 Chirality : 0.044 0.384 4390 Planarity : 0.004 0.065 4725 Dihedral : 7.532 100.927 4771 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 0.97 % Allowed : 10.55 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.15), residues: 3261 helix: 2.19 (0.17), residues: 989 sheet: 0.25 (0.21), residues: 659 loop : -1.33 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 318 TYR 0.016 0.001 TYR B1065 PHE 0.024 0.001 PHE L 438 TRP 0.012 0.001 TRP B 884 HIS 0.008 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00316 (27442) covalent geometry : angle 0.54665 (37331) SS BOND : bond 0.00256 ( 34) SS BOND : angle 1.27136 ( 68) hydrogen bonds : bond 0.05411 ( 1075) hydrogen bonds : angle 4.86749 ( 3061) link_ALPHA1-3 : bond 0.00958 ( 1) link_ALPHA1-3 : angle 2.17713 ( 3) link_ALPHA1-6 : bond 0.00942 ( 1) link_ALPHA1-6 : angle 2.58653 ( 3) link_BETA1-4 : bond 0.00674 ( 15) link_BETA1-4 : angle 2.00655 ( 45) link_NAG-ASN : bond 0.00377 ( 41) link_NAG-ASN : angle 2.14180 ( 123) *********************** 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 167 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.952 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: B 177 MET cc_start: 0.6327 (pmm) cc_final: 0.4764 (ppp) REVERT: B 630 THR cc_start: 0.7374 (p) cc_final: 0.7130 (p) REVERT: C 41 LYS cc_start: 0.8327 (mttt) cc_final: 0.8089 (mttm) REVERT: C 170 TYR cc_start: 0.8172 (t80) cc_final: 0.7786 (t80) REVERT: C 200 TYR cc_start: 0.9129 (m-80) cc_final: 0.8586 (t80) REVERT: C 427 ASP cc_start: 0.8026 (m-30) cc_final: 0.7519 (p0) REVERT: C 451 TRP cc_start: 0.8339 (m100) cc_final: 0.7877 (m100) REVERT: C 514 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7331 (tm-30) REVERT: C 570 THR cc_start: 0.8925 (m) cc_final: 0.8506 (p) REVERT: C 626 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8546 (mm-40) REVERT: L 152 MET cc_start: 0.2736 (mmt) cc_final: 0.2272 (mmt) REVERT: L 270 MET cc_start: 0.3131 (mmt) cc_final: 0.1951 (tpp) outliers start: 28 outliers final: 18 residues processed: 159 average time/residue: 0.1600 time to fit residues: 42.8870 Evaluate side-chains 150 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 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 323 MET 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 171 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 236 optimal weight: 0.0370 chunk 179 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.138206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084825 restraints weight = 77581.349| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.14 r_work: 0.2959 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27534 Z= 0.115 Angle : 0.546 15.784 37573 Z= 0.270 Chirality : 0.044 0.371 4390 Planarity : 0.004 0.067 4725 Dihedral : 7.242 100.501 4771 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.03 % Allowed : 11.14 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.15), residues: 3261 helix: 2.24 (0.17), residues: 986 sheet: 0.28 (0.21), residues: 656 loop : -1.32 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 318 TYR 0.016 0.001 TYR B 170 PHE 0.022 0.001 PHE C 937 TRP 0.012 0.001 TRP B 884 HIS 0.007 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00256 (27442) covalent geometry : angle 0.52599 (37331) SS BOND : bond 0.00221 ( 34) SS BOND : angle 1.31614 ( 68) hydrogen bonds : bond 0.05037 ( 1075) hydrogen bonds : angle 4.76241 ( 3061) link_ALPHA1-3 : bond 0.01002 ( 1) link_ALPHA1-3 : angle 2.20753 ( 3) link_ALPHA1-6 : bond 0.01010 ( 1) link_ALPHA1-6 : angle 2.50647 ( 3) link_BETA1-4 : bond 0.00678 ( 15) link_BETA1-4 : angle 1.92997 ( 45) link_NAG-ASN : bond 0.00389 ( 41) link_NAG-ASN : angle 2.10450 ( 123) *********************** 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 174 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.991 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: B 177 MET cc_start: 0.6189 (pmm) cc_final: 0.4644 (ppp) REVERT: C 41 LYS cc_start: 0.8246 (mttt) cc_final: 0.7990 (mttm) REVERT: C 170 TYR cc_start: 0.8218 (t80) cc_final: 0.7866 (t80) REVERT: C 200 TYR cc_start: 0.9033 (m-80) cc_final: 0.8480 (t80) REVERT: C 236 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7494 (mtp85) REVERT: C 427 ASP cc_start: 0.8035 (m-30) cc_final: 0.7533 (p0) REVERT: C 451 TRP cc_start: 0.8392 (m100) cc_final: 0.7910 (m100) REVERT: C 514 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 570 THR cc_start: 0.8964 (m) cc_final: 0.8564 (p) REVERT: C 626 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8515 (mm-40) REVERT: L 152 MET cc_start: 0.2732 (mmt) cc_final: 0.2468 (mmt) REVERT: L 270 MET cc_start: 0.3156 (mmt) cc_final: 0.1938 (tpp) outliers start: 30 outliers final: 21 residues processed: 165 average time/residue: 0.1667 time to fit residues: 46.2452 Evaluate side-chains 157 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 876 LEU Chi-restraints excluded: chain B residue 914 LEU 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 1048 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 376 MET 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 89 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 175 optimal weight: 30.0000 chunk 261 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 626 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN L 61 ASN L 154 ASN ** L 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 535 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.134111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.080032 restraints weight = 82245.726| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 4.61 r_work: 0.2876 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 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 = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27534 Z= 0.255 Angle : 0.661 20.172 37573 Z= 0.330 Chirality : 0.048 0.559 4390 Planarity : 0.004 0.071 4725 Dihedral : 7.525 102.666 4771 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 1.03 % Allowed : 12.31 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 3261 helix: 1.88 (0.17), residues: 1004 sheet: -0.05 (0.21), residues: 632 loop : -1.47 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 318 TYR 0.020 0.002 TYR C1065 PHE 0.041 0.002 PHE C 904 TRP 0.032 0.002 TRP B 884 HIS 0.007 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00623 (27442) covalent geometry : angle 0.63716 (37331) SS BOND : bond 0.00428 ( 34) SS BOND : angle 1.86060 ( 68) hydrogen bonds : bond 0.06922 ( 1075) hydrogen bonds : angle 5.06796 ( 3061) link_ALPHA1-3 : bond 0.01000 ( 1) link_ALPHA1-3 : angle 2.16744 ( 3) link_ALPHA1-6 : bond 0.00959 ( 1) link_ALPHA1-6 : angle 2.88162 ( 3) link_BETA1-4 : bond 0.00626 ( 15) link_BETA1-4 : angle 2.16012 ( 45) link_NAG-ASN : bond 0.00470 ( 41) link_NAG-ASN : angle 2.53975 ( 123) *********************** 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 163 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6202 (pmm) cc_final: 0.4789 (ppp) REVERT: C 170 TYR cc_start: 0.8014 (t80) cc_final: 0.7608 (t80) REVERT: C 413 GLN cc_start: 0.8635 (tt0) cc_final: 0.8418 (tt0) REVERT: C 427 ASP cc_start: 0.8083 (m-30) cc_final: 0.7574 (p0) REVERT: C 451 TRP cc_start: 0.8376 (m100) cc_final: 0.7897 (m100) REVERT: C 514 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7313 (tm-30) REVERT: C 570 THR cc_start: 0.9028 (m) cc_final: 0.8586 (p) REVERT: C 626 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8429 (mm-40) REVERT: L 152 MET cc_start: 0.3081 (mmt) cc_final: 0.2870 (mmt) REVERT: L 270 MET cc_start: 0.3261 (mmt) cc_final: 0.2142 (tpp) outliers start: 30 outliers final: 24 residues processed: 154 average time/residue: 0.1654 time to fit residues: 42.9433 Evaluate side-chains 148 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 618 VAL 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 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 323 MET Chi-restraints excluded: chain L residue 376 MET 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 255 optimal weight: 0.7980 chunk 271 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 238 GLN C 330 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.131512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075514 restraints weight = 84523.902| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.99 r_work: 0.2927 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 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 = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27534 Z= 0.147 Angle : 0.594 21.716 37573 Z= 0.292 Chirality : 0.045 0.412 4390 Planarity : 0.004 0.070 4725 Dihedral : 7.857 103.754 4771 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 0.97 % Allowed : 12.66 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.15), residues: 3261 helix: 2.00 (0.17), residues: 1001 sheet: 0.06 (0.21), residues: 648 loop : -1.42 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 318 TYR 0.017 0.001 TYR C 902 PHE 0.022 0.001 PHE C 215 TRP 0.022 0.001 TRP B 884 HIS 0.008 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00343 (27442) covalent geometry : angle 0.57124 (37331) SS BOND : bond 0.00270 ( 34) SS BOND : angle 1.57657 ( 68) hydrogen bonds : bond 0.05870 ( 1075) hydrogen bonds : angle 4.90728 ( 3061) link_ALPHA1-3 : bond 0.00989 ( 1) link_ALPHA1-3 : angle 2.16301 ( 3) link_ALPHA1-6 : bond 0.01055 ( 1) link_ALPHA1-6 : angle 2.44087 ( 3) link_BETA1-4 : bond 0.00673 ( 15) link_BETA1-4 : angle 1.99934 ( 45) link_NAG-ASN : bond 0.00337 ( 41) link_NAG-ASN : angle 2.34172 ( 123) *********************** 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 161 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6155 (pmm) cc_final: 0.4711 (ppp) REVERT: B 634 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.6280 (t80) REVERT: B 688 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8122 (mp10) REVERT: C 41 LYS cc_start: 0.8355 (mttt) cc_final: 0.8135 (mttt) REVERT: C 170 TYR cc_start: 0.8225 (t80) cc_final: 0.7856 (t80) REVERT: C 427 ASP cc_start: 0.8021 (m-30) cc_final: 0.7517 (p0) REVERT: C 451 TRP cc_start: 0.8319 (m100) cc_final: 0.7867 (m100) REVERT: C 514 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7278 (tm-30) REVERT: C 570 THR cc_start: 0.8989 (m) cc_final: 0.8569 (p) REVERT: C 626 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8369 (mm-40) REVERT: L 516 TYR cc_start: 0.8508 (t80) cc_final: 0.8021 (m-80) outliers start: 28 outliers final: 24 residues processed: 155 average time/residue: 0.1625 time to fit residues: 41.9751 Evaluate side-chains 154 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 634 TYR 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 L residue 82 MET Chi-restraints excluded: chain L residue 274 PHE Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 376 MET 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 280 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 315 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 250 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** L 42 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.131390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.076653 restraints weight = 95479.878| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.90 r_work: 0.2913 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 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 = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27534 Z= 0.131 Angle : 0.588 20.368 37573 Z= 0.288 Chirality : 0.045 0.544 4390 Planarity : 0.004 0.069 4725 Dihedral : 7.953 109.009 4771 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 0.97 % Allowed : 12.76 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3261 helix: 2.13 (0.17), residues: 990 sheet: 0.11 (0.20), residues: 655 loop : -1.40 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.016 0.001 TYR B1065 PHE 0.022 0.001 PHE C 215 TRP 0.019 0.001 TRP B 631 HIS 0.008 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00297 (27442) covalent geometry : angle 0.56710 (37331) SS BOND : bond 0.00228 ( 34) SS BOND : angle 1.44595 ( 68) hydrogen bonds : bond 0.05441 ( 1075) hydrogen bonds : angle 4.81844 ( 3061) link_ALPHA1-3 : bond 0.00976 ( 1) link_ALPHA1-3 : angle 2.21011 ( 3) link_ALPHA1-6 : bond 0.01046 ( 1) link_ALPHA1-6 : angle 2.27662 ( 3) link_BETA1-4 : bond 0.00679 ( 15) link_BETA1-4 : angle 1.93794 ( 45) link_NAG-ASN : bond 0.00327 ( 41) link_NAG-ASN : angle 2.32478 ( 123) *********************** 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 163 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6118 (pmm) cc_final: 0.4667 (ppp) REVERT: B 634 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6162 (t80) REVERT: B 688 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: C 41 LYS cc_start: 0.8351 (mttt) cc_final: 0.8076 (mttt) REVERT: C 170 TYR cc_start: 0.8104 (t80) cc_final: 0.7726 (t80) REVERT: C 427 ASP cc_start: 0.8064 (m-30) cc_final: 0.7567 (p0) REVERT: C 451 TRP cc_start: 0.8382 (m100) cc_final: 0.7898 (m100) REVERT: C 514 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 570 THR cc_start: 0.8901 (m) cc_final: 0.8465 (p) REVERT: C 626 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8369 (mm-40) REVERT: L 516 TYR cc_start: 0.8286 (t80) cc_final: 0.7815 (m-80) outliers start: 28 outliers final: 24 residues processed: 156 average time/residue: 0.1677 time to fit residues: 43.5427 Evaluate side-chains 154 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 634 TYR 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 933 GLN Chi-restraints excluded: chain C residue 971 ILE Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 274 PHE Chi-restraints excluded: chain L residue 283 VAL Chi-restraints excluded: chain L residue 323 MET Chi-restraints excluded: chain L residue 376 MET 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 152 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 269 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 238 GLN C 330 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.130250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.075601 restraints weight = 98122.193| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.89 r_work: 0.2896 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 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 = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27534 Z= 0.161 Angle : 0.593 15.243 37573 Z= 0.295 Chirality : 0.045 0.472 4390 Planarity : 0.004 0.070 4725 Dihedral : 7.889 108.544 4771 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 0.97 % Allowed : 12.90 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.15), residues: 3261 helix: 2.15 (0.17), residues: 985 sheet: 0.06 (0.21), residues: 646 loop : -1.39 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 236 TYR 0.018 0.001 TYR C 902 PHE 0.020 0.001 PHE C 904 TRP 0.022 0.001 TRP B 884 HIS 0.013 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00383 (27442) covalent geometry : angle 0.57254 (37331) SS BOND : bond 0.00252 ( 34) SS BOND : angle 1.53053 ( 68) hydrogen bonds : bond 0.05723 ( 1075) hydrogen bonds : angle 4.81230 ( 3061) link_ALPHA1-3 : bond 0.00961 ( 1) link_ALPHA1-3 : angle 2.17401 ( 3) link_ALPHA1-6 : bond 0.00955 ( 1) link_ALPHA1-6 : angle 2.26429 ( 3) link_BETA1-4 : bond 0.00679 ( 15) link_BETA1-4 : angle 1.97086 ( 45) link_NAG-ASN : bond 0.00381 ( 41) link_NAG-ASN : angle 2.24538 ( 123) ********************** 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: 28 poor density : 128 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6111 (pmm) cc_final: 0.4678 (ppp) REVERT: B 634 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6273 (t80) REVERT: B 688 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: C 41 LYS cc_start: 0.8404 (mttt) cc_final: 0.8106 (mttm) REVERT: C 200 TYR cc_start: 0.8994 (m-80) cc_final: 0.8457 (t80) REVERT: C 413 GLN cc_start: 0.8584 (tt0) cc_final: 0.8316 (tt0) REVERT: C 427 ASP cc_start: 0.8084 (m-30) cc_final: 0.7578 (p0) REVERT: C 451 TRP cc_start: 0.8373 (m100) cc_final: 0.7906 (m100) REVERT: C 514 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7292 (tm-30) REVERT: C 570 THR cc_start: 0.8899 (m) cc_final: 0.8455 (p) REVERT: C 626 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8341 (mm-40) REVERT: L 480 MET cc_start: 0.6727 (mmt) cc_final: 0.6472 (mpp) REVERT: L 516 TYR cc_start: 0.8302 (t80) cc_final: 0.7803 (m-80) REVERT: L 530 CYS cc_start: 0.5836 (p) cc_final: 0.5446 (p) outliers start: 28 outliers final: 26 residues processed: 149 average time/residue: 0.1792 time to fit residues: 44.5509 Evaluate side-chains 155 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 634 TYR 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 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 323 MET Chi-restraints excluded: chain L residue 376 MET 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 259 optimal weight: 0.2980 chunk 254 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 303 optimal weight: 50.0000 chunk 2 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 238 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.134004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078418 restraints weight = 95538.308| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.92 r_work: 0.2887 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 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 = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27534 Z= 0.147 Angle : 0.583 15.342 37573 Z= 0.288 Chirality : 0.045 0.403 4390 Planarity : 0.004 0.070 4725 Dihedral : 7.728 107.911 4771 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 1.10 % Allowed : 12.79 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 3261 helix: 2.17 (0.17), residues: 985 sheet: 0.09 (0.21), residues: 650 loop : -1.40 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 236 TYR 0.017 0.001 TYR B1065 PHE 0.020 0.001 PHE C 904 TRP 0.021 0.001 TRP B 884 HIS 0.012 0.001 HIS L 401 Details of bonding type rmsd covalent geometry : bond 0.00347 (27442) covalent geometry : angle 0.56317 (37331) SS BOND : bond 0.00240 ( 34) SS BOND : angle 1.46469 ( 68) hydrogen bonds : bond 0.05548 ( 1075) hydrogen bonds : angle 4.75833 ( 3061) link_ALPHA1-3 : bond 0.00933 ( 1) link_ALPHA1-3 : angle 2.13927 ( 3) link_ALPHA1-6 : bond 0.01096 ( 1) link_ALPHA1-6 : angle 2.29321 ( 3) link_BETA1-4 : bond 0.00663 ( 15) link_BETA1-4 : angle 1.93363 ( 45) link_NAG-ASN : bond 0.00353 ( 41) link_NAG-ASN : angle 2.14878 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9668.77 seconds wall clock time: 165 minutes 53.80 seconds (9953.80 seconds total)