Starting phenix.real_space_refine on Tue Jun 17 22:26:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bf6_44491/06_2025/9bf6_44491.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bf6_44491/06_2025/9bf6_44491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bf6_44491/06_2025/9bf6_44491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bf6_44491/06_2025/9bf6_44491.map" model { file = "/net/cci-nas-00/data/ceres_data/9bf6_44491/06_2025/9bf6_44491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bf6_44491/06_2025/9bf6_44491.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 120 5.16 5 C 12732 2.51 5 N 3318 2.21 5 O 4159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20330 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 973 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3390 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 6 Chain: "D" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 973 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3390 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 6 Chain: "G" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "H" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "I" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 973 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "J" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3390 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 407} Chain breaks: 6 Chain: "K" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" 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: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" 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: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" 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: "T" 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: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" 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: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" 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: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" 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: "a" 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: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" 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: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" 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: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 159 Unusual residues: {'NAG': 11, 'PO4': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" 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: 13.69, per 1000 atoms: 0.67 Number of scatterers: 20330 At special positions: 0 Unit cell: (155.629, 154.555, 150.262, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 1 15.00 O 4159 8.00 N 3318 7.00 C 12732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 432A" distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 432A" distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.04 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.04 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 432A" distance=2.04 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.04 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.05 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN P 4 " - " MAN P 5 " " MAN U 4 " - " MAN U 5 " " MAN W 4 " - " MAN W 5 " " MAN b 4 " - " MAN b 5 " " MAN d 4 " - " MAN d 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 6 " " BMA W 3 " - " MAN W 6 " " BMA b 3 " - " MAN b 6 " " BMA d 3 " - " MAN d 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " NAG-ASN " NAG A 701 " - " ASN A 637 " " NAG A 702 " - " ASN A 611 " " NAG A 703 " - " ASN A 625 " " NAG A 704 " - " ASN A 616 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 616 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 276 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 362 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 133 " " NAG C 609 " - " ASN C 413 " " NAG C 610 " - " ASN C 392 " " NAG C 611 " - " ASN C 230 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 276 " " NAG F 603 " - " ASN F 295 " " NAG F 604 " - " ASN F 301 " " NAG F 605 " - " ASN F 362 " " NAG F 606 " - " ASN F 386 " " NAG F 607 " - " ASN F 448 " " NAG F 608 " - " ASN F 133 " " NAG F 609 " - " ASN F 413 " " NAG F 610 " - " ASN F 392 " " NAG F 611 " - " ASN F 230 " " NAG I 701 " - " ASN I 637 " " NAG I 702 " - " ASN I 611 " " NAG I 703 " - " ASN I 625 " " NAG I 704 " - " ASN I 616 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 276 " " NAG J 603 " - " ASN J 295 " " NAG J 604 " - " ASN J 301 " " NAG J 605 " - " ASN J 362 " " NAG J 606 " - " ASN J 386 " " NAG J 607 " - " ASN J 448 " " NAG J 608 " - " ASN J 133 " " NAG J 609 " - " ASN J 413 " " NAG J 610 " - " ASN J 392 " " NAG J 611 " - " ASN J 230 " " NAG M 1 " - " ASN C 241 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN C 49 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN C 160 " " NAG R 1 " - " ASN C 156 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN F 241 " " NAG U 1 " - " ASN F 262 " " NAG V 1 " - " ASN F 49 " " NAG W 1 " - " ASN F 332 " " NAG X 1 " - " ASN F 160 " " NAG Y 1 " - " ASN F 156 " " NAG Z 1 " - " ASN F 197 " " NAG a 1 " - " ASN J 241 " " NAG b 1 " - " ASN J 262 " " NAG c 1 " - " ASN J 49 " " NAG d 1 " - " ASN J 332 " " NAG e 1 " - " ASN J 160 " " NAG f 1 " - " ASN J 156 " " NAG g 1 " - " ASN J 197 " Time building additional restraints: 6.22 Conformation dependent library (CDL) restraints added in 2.5 seconds 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4380 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 42 sheets defined 15.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.662A pdb=" N VAL A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.691A pdb=" N VAL A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.895A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 661 removed outlier: 4.228A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 336 through 353 removed outlier: 3.524A pdb=" N GLN C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.666A pdb=" N MET C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.844A pdb=" N GLU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 removed outlier: 4.710A pdb=" N VAL B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.539A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.922A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 661 removed outlier: 4.280A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 115 Processing helix chain 'F' and resid 336 through 353 removed outlier: 4.355A pdb=" N GLU F 351 " --> pdb=" O ASP F 347 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.655A pdb=" N MET F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.818A pdb=" N GLU H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 535 No H-bonds generated for 'chain 'I' and resid 533 through 535' Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.515A pdb=" N LEU I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 596 removed outlier: 3.613A pdb=" N VAL I 580 " --> pdb=" O LEU I 576 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU I 581 " --> pdb=" O GLN I 577 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA I 582 " --> pdb=" O ALA I 578 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I 592 " --> pdb=" O LYS I 588 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU I 593 " --> pdb=" O ASP I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 661 removed outlier: 3.723A pdb=" N ILE I 635 " --> pdb=" O TRP I 631 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN I 637 " --> pdb=" O ARG I 633 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TYR I 638 " --> pdb=" O GLU I 634 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY I 640 " --> pdb=" O ASP I 636 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE I 641 " --> pdb=" O ASN I 637 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE I 642 " --> pdb=" O TYR I 638 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR I 643 " --> pdb=" O THR I 639 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR I 644 " --> pdb=" O GLY I 640 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU I 647 " --> pdb=" O TYR I 643 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN I 652 " --> pdb=" O GLU I 648 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN I 653 " --> pdb=" O SER I 649 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU I 658 " --> pdb=" O GLU I 654 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU I 659 " --> pdb=" O LYS I 655 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 115 Processing helix chain 'J' and resid 336 through 353 removed outlier: 3.672A pdb=" N GLN J 344 " --> pdb=" O ASN J 340 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU J 351 " --> pdb=" O ASP J 347 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN J 352 " --> pdb=" O LYS J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.644A pdb=" N MET J 373 " --> pdb=" O PRO J 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.640A pdb=" N ASP K 86 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER K 87 " --> pdb=" O ALA K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.764A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 604 through 605 removed outlier: 3.754A pdb=" N VAL C 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.209A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.562A pdb=" N LEU C 129 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR C 191 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 3.610A pdb=" N TYR C 435 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 271 through 272 removed outlier: 3.757A pdb=" N ILE C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 374 through 375 removed outlier: 3.570A pdb=" N ILE C 414 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 302 through 306 removed outlier: 6.478A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.290A pdb=" N ILE C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.680A pdb=" N THR D 105 " --> pdb=" O TYR D 90 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 90 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 107 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR D 33 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.706A pdb=" N VAL E 13 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N TRP E 35 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU E 46 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN E 37 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG E 39 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 18 through 22 removed outlier: 4.204A pdb=" N THR E 74 " --> pdb=" O SER E 63 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER E 63 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 40 Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 46 removed outlier: 4.241A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 91 through 92 Processing sheet with id=AB9, first strand: chain 'F' and resid 129 through 130 removed outlier: 4.133A pdb=" N TYR F 191 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AC2, first strand: chain 'F' and resid 201 through 203 removed outlier: 3.597A pdb=" N TYR F 435 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 271 through 272 removed outlier: 3.663A pdb=" N ILE F 271 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 374 through 375 Processing sheet with id=AC5, first strand: chain 'F' and resid 302 through 306 removed outlier: 6.487A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 319 " --> pdb=" O ARG F 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 360 through 361 removed outlier: 6.393A pdb=" N ILE F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.704A pdb=" N THR G 105 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR G 90 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 107 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR G 33 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TRP G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AC9, first strand: chain 'H' and resid 9 through 13 removed outlier: 3.674A pdb=" N VAL H 13 " --> pdb=" O ILE H 105 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N TRP H 35 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU H 46 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN H 37 " --> pdb=" O PRO H 44 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG H 39 " --> pdb=" O GLN H 42 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 19 through 22 removed outlier: 4.194A pdb=" N THR H 74 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER H 63 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 37 through 40 Processing sheet with id=AD3, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AD4, first strand: chain 'J' and resid 91 through 92 Processing sheet with id=AD5, first strand: chain 'J' and resid 129 through 130 removed outlier: 4.148A pdb=" N TYR J 191 " --> pdb=" O LEU J 129 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 157 through 158 Processing sheet with id=AD7, first strand: chain 'J' and resid 201 through 203 removed outlier: 3.684A pdb=" N TYR J 435 " --> pdb=" O THR J 202 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 271 through 272 removed outlier: 3.723A pdb=" N ILE J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 374 through 375 removed outlier: 3.573A pdb=" N ILE J 414 " --> pdb=" O ILE J 333 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE J 333 " --> pdb=" O ILE J 414 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 302 through 306 removed outlier: 6.356A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA J 319 " --> pdb=" O ARG J 305 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 360 through 361 removed outlier: 6.464A pdb=" N ILE J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.771A pdb=" N THR K 105 " --> pdb=" O TYR K 90 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR K 90 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL K 107 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA K 88 " --> pdb=" O VAL K 107 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR K 33 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR K 50 " --> pdb=" O TRP K 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 18 through 22 Processing sheet with id=AE5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.546A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TRP L 35 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU L 46 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN L 37 " --> pdb=" O PRO L 44 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG L 39 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 19 through 22 removed outlier: 4.190A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1140 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: 6.35 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6142 1.34 - 1.47: 5448 1.47 - 1.59: 8988 1.59 - 1.71: 0 1.71 - 1.84: 162 Bond restraints: 20740 Sorted by residual: bond pdb=" O3 PO4 F 612 " pdb=" P PO4 F 612 " ideal model delta sigma weight residual 1.569 1.521 0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" O4 PO4 F 612 " pdb=" P PO4 F 612 " ideal model delta sigma weight residual 1.568 1.522 0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" O2 PO4 F 612 " pdb=" P PO4 F 612 " ideal model delta sigma weight residual 1.567 1.523 0.044 2.00e-02 2.50e+03 4.95e+00 bond pdb=" O1 PO4 F 612 " pdb=" P PO4 F 612 " ideal model delta sigma weight residual 1.565 1.522 0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" N GLN G 1 " pdb=" CA GLN G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 ... (remaining 20735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 27358 1.76 - 3.51: 679 3.51 - 5.27: 132 5.27 - 7.02: 15 7.02 - 8.78: 4 Bond angle restraints: 28188 Sorted by residual: angle pdb=" N THR J 162 " pdb=" CA THR J 162 " pdb=" C THR J 162 " ideal model delta sigma weight residual 110.24 119.02 -8.78 1.41e+00 5.03e-01 3.88e+01 angle pdb=" C THR C 163 " pdb=" CA THR C 163 " pdb=" CB THR C 163 " ideal model delta sigma weight residual 110.06 102.93 7.13 1.44e+00 4.82e-01 2.46e+01 angle pdb=" N THR C 163 " pdb=" CA THR C 163 " pdb=" C THR C 163 " ideal model delta sigma weight residual 113.28 120.94 -7.66 1.57e+00 4.06e-01 2.38e+01 angle pdb=" N ASP C 167 " pdb=" CA ASP C 167 " pdb=" C ASP C 167 " ideal model delta sigma weight residual 108.38 113.83 -5.45 1.35e+00 5.49e-01 1.63e+01 angle pdb=" N THR C 163 " pdb=" CA THR C 163 " pdb=" CB THR C 163 " ideal model delta sigma weight residual 114.17 109.79 4.38 1.14e+00 7.69e-01 1.48e+01 ... (remaining 28183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12708 17.88 - 35.75: 1015 35.75 - 53.63: 232 53.63 - 71.50: 33 71.50 - 89.38: 16 Dihedral angle restraints: 14004 sinusoidal: 7206 harmonic: 6798 Sorted by residual: dihedral pdb=" CB CYS J 228 " pdb=" SG CYS J 228 " pdb=" SG CYS J 239 " pdb=" CB CYS J 239 " ideal model delta sinusoidal sigma weight residual 93.00 4.49 88.51 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS J 113 " pdb=" SG CYS J 113 " pdb=" SG CYS J 432A" pdb=" CB CYS J 432A" ideal model delta sinusoidal sigma weight residual 93.00 179.31 -86.31 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS C 113 " pdb=" SG CYS C 113 " pdb=" SG CYS C 432A" pdb=" CB CYS C 432A" ideal model delta sinusoidal sigma weight residual 93.00 170.79 -77.79 1 1.00e+01 1.00e-02 7.57e+01 ... (remaining 14001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3272 0.089 - 0.177: 274 0.177 - 0.266: 5 0.266 - 0.354: 0 0.354 - 0.443: 7 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CA THR C 162 " pdb=" N THR C 162 " pdb=" C THR C 162 " pdb=" CB THR C 162 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA THR J 162 " pdb=" N THR J 162 " pdb=" C THR J 162 " pdb=" CB THR J 162 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 637 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 3555 not shown) Planarity restraints: 3450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 94 " 0.321 9.50e-02 1.11e+02 1.44e-01 1.28e+01 pdb=" NE ARG E 94 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG E 94 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG E 94 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 94 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 117 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO J 118 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO J 118 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 118 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 117 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO F 118 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO F 118 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 118 " -0.034 5.00e-02 4.00e+02 ... (remaining 3447 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 223 2.60 - 3.17: 17456 3.17 - 3.75: 28706 3.75 - 4.32: 38090 4.32 - 4.90: 62688 Nonbonded interactions: 147163 Sorted by model distance: nonbonded pdb=" OG1 THR A 538 " pdb=" OE1 GLU B 647 " model vdw 2.022 3.040 nonbonded pdb=" OG SER J 334 " pdb=" OE1 GLU J 336 " model vdw 2.087 3.040 nonbonded pdb=" OG SER J 256 " pdb=" O LEU J 259 " model vdw 2.169 3.040 nonbonded pdb=" NH2 ARG A 585 " pdb=" O ILE C 491 " model vdw 2.171 3.120 nonbonded pdb=" OG SER K 70 " pdb=" OG SER K 79 " model vdw 2.171 3.040 ... (remaining 147158 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' selection = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = (chain 'F' and (resid 32 through 505 or resid 601 through 611)) selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'U' selection = chain 'W' selection = chain 'b' selection = chain 'd' } ncs_group { reference = chain 'R' selection = chain 'Y' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 48.330 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.060 20908 Z= 0.146 Angle : 0.714 8.779 28653 Z= 0.350 Chirality : 0.047 0.443 3558 Planarity : 0.005 0.144 3384 Dihedral : 12.768 89.376 9507 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.43 % Favored : 91.40 % Rotamer: Outliers : 0.10 % Allowed : 0.24 % Favored : 99.66 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2301 helix: -0.64 (0.29), residues: 315 sheet: 0.00 (0.23), residues: 543 loop : -1.62 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 479 HIS 0.005 0.001 HIS F 216 PHE 0.011 0.001 PHE F 159 TYR 0.020 0.001 TYR F 435 ARG 0.009 0.000 ARG J 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 66) link_NAG-ASN : angle 2.28390 ( 198) link_ALPHA1-6 : bond 0.01123 ( 6) link_ALPHA1-6 : angle 1.54284 ( 18) link_BETA1-4 : bond 0.00676 ( 42) link_BETA1-4 : angle 2.17717 ( 126) link_ALPHA1-2 : bond 0.00803 ( 6) link_ALPHA1-2 : angle 2.99816 ( 18) link_ALPHA1-3 : bond 0.01001 ( 9) link_ALPHA1-3 : angle 2.07537 ( 27) hydrogen bonds : bond 0.27506 ( 437) hydrogen bonds : angle 8.72546 ( 1140) SS BOND : bond 0.00534 ( 39) SS BOND : angle 1.43173 ( 78) covalent geometry : bond 0.00311 (20740) covalent geometry : angle 0.66563 (28188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 ASP cc_start: 0.9319 (m-30) cc_final: 0.8717 (p0) REVERT: A 595 ILE cc_start: 0.9638 (mm) cc_final: 0.8986 (tt) REVERT: C 215 ILE cc_start: 0.9561 (pt) cc_final: 0.9189 (mp) REVERT: C 284 ILE cc_start: 0.9254 (mm) cc_final: 0.8841 (tt) REVERT: C 373 MET cc_start: 0.9088 (mtm) cc_final: 0.8804 (ptp) REVERT: D 30 ARG cc_start: 0.9425 (tmm-80) cc_final: 0.9191 (mpt180) REVERT: D 90 TYR cc_start: 0.8868 (m-80) cc_final: 0.8648 (m-80) REVERT: B 589 ASP cc_start: 0.9510 (m-30) cc_final: 0.8778 (p0) REVERT: B 595 ILE cc_start: 0.9491 (mm) cc_final: 0.9259 (mt) REVERT: F 215 ILE cc_start: 0.9612 (pt) cc_final: 0.9302 (mp) REVERT: F 284 ILE cc_start: 0.9296 (mm) cc_final: 0.8830 (tt) REVERT: G 30 ARG cc_start: 0.9304 (tmm-80) cc_final: 0.9022 (mtm-85) REVERT: G 31 ASP cc_start: 0.9555 (t0) cc_final: 0.9319 (m-30) REVERT: I 589 ASP cc_start: 0.9513 (m-30) cc_final: 0.8953 (p0) REVERT: I 595 ILE cc_start: 0.9573 (mm) cc_final: 0.8966 (tp) REVERT: J 454 LEU cc_start: 0.9535 (mt) cc_final: 0.9317 (mt) REVERT: K 31 ASP cc_start: 0.9546 (t0) cc_final: 0.9341 (m-30) REVERT: K 90 TYR cc_start: 0.8724 (m-80) cc_final: 0.8324 (m-80) REVERT: K 100 MET cc_start: 0.9714 (mpp) cc_final: 0.9444 (mmp) REVERT: L 90 ILE cc_start: 0.9588 (pt) cc_final: 0.9302 (mp) outliers start: 2 outliers final: 0 residues processed: 220 average time/residue: 0.3910 time to fit residues: 124.5896 Evaluate side-chains 116 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 183 optimal weight: 4.9990 chunk 70 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN C 389 GLN D 3 HIS D 76 ASN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS G 68 HIS G 76 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 GLN I 577 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.035526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.028700 restraints weight = 337736.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.029424 restraints weight = 204826.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.029914 restraints weight = 143662.092| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20908 Z= 0.177 Angle : 0.746 13.204 28653 Z= 0.348 Chirality : 0.049 0.377 3558 Planarity : 0.004 0.060 3384 Dihedral : 8.508 59.225 5154 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.13 % Favored : 91.70 % Rotamer: Outliers : 0.19 % Allowed : 4.76 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2301 helix: -0.69 (0.26), residues: 330 sheet: 0.11 (0.24), residues: 489 loop : -1.71 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 101 HIS 0.004 0.001 HIS J 374 PHE 0.025 0.001 PHE J 159 TYR 0.013 0.001 TYR C 217 ARG 0.008 0.001 ARG J 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 66) link_NAG-ASN : angle 2.93258 ( 198) link_ALPHA1-6 : bond 0.00762 ( 6) link_ALPHA1-6 : angle 1.62670 ( 18) link_BETA1-4 : bond 0.00704 ( 42) link_BETA1-4 : angle 2.19579 ( 126) link_ALPHA1-2 : bond 0.00952 ( 6) link_ALPHA1-2 : angle 3.23399 ( 18) link_ALPHA1-3 : bond 0.00955 ( 9) link_ALPHA1-3 : angle 2.01927 ( 27) hydrogen bonds : bond 0.05363 ( 437) hydrogen bonds : angle 6.03191 ( 1140) SS BOND : bond 0.00210 ( 39) SS BOND : angle 1.00687 ( 78) covalent geometry : bond 0.00366 (20740) covalent geometry : angle 0.68474 (28188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 2.201 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 626 MET cc_start: 0.8693 (tmm) cc_final: 0.8405 (tmm) REVERT: B 530 MET cc_start: 0.7415 (mmp) cc_final: 0.6979 (mmm) REVERT: B 595 ILE cc_start: 0.9384 (mm) cc_final: 0.9141 (mt) REVERT: B 626 MET cc_start: 0.8378 (ppp) cc_final: 0.7046 (ppp) REVERT: F 154 MET cc_start: 0.7582 (mmp) cc_final: 0.6687 (mmp) REVERT: G 90 TYR cc_start: 0.8775 (m-10) cc_final: 0.8569 (m-10) REVERT: H 85 ASP cc_start: 0.8949 (t0) cc_final: 0.8596 (t0) REVERT: I 595 ILE cc_start: 0.9590 (mm) cc_final: 0.9169 (tt) REVERT: I 626 MET cc_start: 0.8694 (ppp) cc_final: 0.7546 (ppp) REVERT: J 150 MET cc_start: 0.7145 (pmm) cc_final: 0.6250 (tpp) REVERT: J 163 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9163 (m) REVERT: J 454 LEU cc_start: 0.9551 (mt) cc_final: 0.9302 (mt) REVERT: K 90 TYR cc_start: 0.8783 (m-80) cc_final: 0.8581 (m-10) REVERT: K 100 MET cc_start: 0.9349 (mpp) cc_final: 0.8763 (mpp) REVERT: L 90 ILE cc_start: 0.9554 (pt) cc_final: 0.9275 (mp) outliers start: 4 outliers final: 2 residues processed: 142 average time/residue: 0.3599 time to fit residues: 76.7378 Evaluate side-chains 96 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 120 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 199 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 222 optimal weight: 0.0570 chunk 114 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.035240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.028463 restraints weight = 336691.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.029186 restraints weight = 202603.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.029686 restraints weight = 141292.473| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20908 Z= 0.141 Angle : 0.697 13.961 28653 Z= 0.321 Chirality : 0.048 0.390 3558 Planarity : 0.004 0.048 3384 Dihedral : 8.290 59.992 5154 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.65 % Favored : 92.18 % Rotamer: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2301 helix: -0.05 (0.28), residues: 312 sheet: 0.06 (0.24), residues: 474 loop : -1.61 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 338 HIS 0.004 0.001 HIS C 374 PHE 0.010 0.001 PHE C 233 TYR 0.012 0.001 TYR C 217 ARG 0.004 0.000 ARG D 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00760 ( 66) link_NAG-ASN : angle 2.96097 ( 198) link_ALPHA1-6 : bond 0.00783 ( 6) link_ALPHA1-6 : angle 1.39585 ( 18) link_BETA1-4 : bond 0.00690 ( 42) link_BETA1-4 : angle 1.98797 ( 126) link_ALPHA1-2 : bond 0.01088 ( 6) link_ALPHA1-2 : angle 3.26523 ( 18) link_ALPHA1-3 : bond 0.00950 ( 9) link_ALPHA1-3 : angle 1.81322 ( 27) hydrogen bonds : bond 0.04419 ( 437) hydrogen bonds : angle 5.52035 ( 1140) SS BOND : bond 0.00289 ( 39) SS BOND : angle 1.05062 ( 78) covalent geometry : bond 0.00296 (20740) covalent geometry : angle 0.63225 (28188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 2.184 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 584 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9183 (pm20) REVERT: C 373 MET cc_start: 0.9122 (pmm) cc_final: 0.8721 (pmm) REVERT: D 90 TYR cc_start: 0.9110 (m-10) cc_final: 0.8831 (m-10) REVERT: E 85 ASP cc_start: 0.8990 (t0) cc_final: 0.8677 (t0) REVERT: B 589 ASP cc_start: 0.9267 (m-30) cc_final: 0.8656 (p0) REVERT: B 595 ILE cc_start: 0.9373 (mm) cc_final: 0.9061 (tp) REVERT: B 626 MET cc_start: 0.8691 (ppp) cc_final: 0.7969 (tmm) REVERT: F 154 MET cc_start: 0.8076 (mmp) cc_final: 0.7491 (mmm) REVERT: I 530 MET cc_start: 0.8354 (mmm) cc_final: 0.7792 (mmp) REVERT: I 595 ILE cc_start: 0.9585 (mm) cc_final: 0.9199 (tt) REVERT: I 626 MET cc_start: 0.8889 (ppp) cc_final: 0.7215 (ppp) REVERT: J 150 MET cc_start: 0.6881 (pmm) cc_final: 0.6190 (tpp) REVERT: J 454 LEU cc_start: 0.9526 (mt) cc_final: 0.9263 (mt) REVERT: L 90 ILE cc_start: 0.9547 (pt) cc_final: 0.9271 (mp) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.3930 time to fit residues: 71.6168 Evaluate side-chains 100 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 145 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN E 17 GLN B 577 GLN B 656 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 302 ASN K 1 GLN K 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.032860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.026154 restraints weight = 353609.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.026822 restraints weight = 213509.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.027277 restraints weight = 150879.559| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20908 Z= 0.211 Angle : 0.776 12.188 28653 Z= 0.360 Chirality : 0.049 0.409 3558 Planarity : 0.004 0.043 3384 Dihedral : 8.351 57.719 5154 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.74 % Favored : 91.09 % Rotamer: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2301 helix: -0.10 (0.27), residues: 342 sheet: -0.11 (0.24), residues: 489 loop : -1.66 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 479 HIS 0.006 0.001 HIS C 374 PHE 0.013 0.002 PHE C 233 TYR 0.016 0.002 TYR A 586 ARG 0.005 0.001 ARG K 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00830 ( 66) link_NAG-ASN : angle 3.08153 ( 198) link_ALPHA1-6 : bond 0.00721 ( 6) link_ALPHA1-6 : angle 1.46846 ( 18) link_BETA1-4 : bond 0.00785 ( 42) link_BETA1-4 : angle 2.03204 ( 126) link_ALPHA1-2 : bond 0.00768 ( 6) link_ALPHA1-2 : angle 3.19972 ( 18) link_ALPHA1-3 : bond 0.00776 ( 9) link_ALPHA1-3 : angle 2.12390 ( 27) hydrogen bonds : bond 0.04167 ( 437) hydrogen bonds : angle 5.54807 ( 1140) SS BOND : bond 0.00289 ( 39) SS BOND : angle 1.21288 ( 78) covalent geometry : bond 0.00434 (20740) covalent geometry : angle 0.71492 (28188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8371 (mmm) cc_final: 0.8030 (mmm) REVERT: A 626 MET cc_start: 0.7685 (tmm) cc_final: 0.6224 (ppp) REVERT: A 629 MET cc_start: 0.9520 (mmp) cc_final: 0.9272 (mmp) REVERT: C 373 MET cc_start: 0.9532 (pmm) cc_final: 0.9038 (pmm) REVERT: D 90 TYR cc_start: 0.9320 (m-10) cc_final: 0.9045 (m-10) REVERT: B 577 GLN cc_start: 0.9528 (mm110) cc_final: 0.9312 (mm110) REVERT: B 589 ASP cc_start: 0.9621 (m-30) cc_final: 0.9387 (m-30) REVERT: B 595 ILE cc_start: 0.9653 (mm) cc_final: 0.9248 (tt) REVERT: B 626 MET cc_start: 0.6178 (ppp) cc_final: 0.4545 (ppp) REVERT: B 629 MET cc_start: 0.9505 (mmp) cc_final: 0.9240 (mmp) REVERT: F 104 MET cc_start: 0.9533 (ppp) cc_final: 0.9264 (ppp) REVERT: F 154 MET cc_start: 0.8694 (mmp) cc_final: 0.8285 (mmm) REVERT: I 589 ASP cc_start: 0.9427 (m-30) cc_final: 0.9160 (m-30) REVERT: I 626 MET cc_start: 0.7987 (ppp) cc_final: 0.7622 (tmm) REVERT: J 100 MET cc_start: 0.9345 (mtm) cc_final: 0.9088 (mtm) REVERT: J 150 MET cc_start: 0.7257 (pmm) cc_final: 0.6660 (tpp) REVERT: J 154 MET cc_start: 0.8002 (mmp) cc_final: 0.7757 (mmp) REVERT: K 90 TYR cc_start: 0.9063 (m-80) cc_final: 0.8563 (m-10) REVERT: K 100 MET cc_start: 0.9513 (mpp) cc_final: 0.8783 (mpp) outliers start: 3 outliers final: 2 residues processed: 113 average time/residue: 0.3744 time to fit residues: 64.1740 Evaluate side-chains 91 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 129 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 194 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 1 GLN D 3 HIS B 656 ASN F 33 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 3 HIS ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 287 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.032470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.025875 restraints weight = 353101.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.026525 restraints weight = 211402.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.026979 restraints weight = 149007.915| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20908 Z= 0.174 Angle : 0.722 15.443 28653 Z= 0.335 Chirality : 0.049 0.436 3558 Planarity : 0.004 0.043 3384 Dihedral : 8.466 59.375 5154 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.04 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2301 helix: -0.00 (0.27), residues: 342 sheet: -0.08 (0.25), residues: 477 loop : -1.66 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 479 HIS 0.004 0.001 HIS F 216 PHE 0.013 0.001 PHE C 233 TYR 0.015 0.001 TYR C 217 ARG 0.004 0.000 ARG J 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 66) link_NAG-ASN : angle 3.05860 ( 198) link_ALPHA1-6 : bond 0.00790 ( 6) link_ALPHA1-6 : angle 1.34971 ( 18) link_BETA1-4 : bond 0.00555 ( 42) link_BETA1-4 : angle 1.77800 ( 126) link_ALPHA1-2 : bond 0.00672 ( 6) link_ALPHA1-2 : angle 3.28941 ( 18) link_ALPHA1-3 : bond 0.00837 ( 9) link_ALPHA1-3 : angle 1.82310 ( 27) hydrogen bonds : bond 0.03774 ( 437) hydrogen bonds : angle 5.34673 ( 1140) SS BOND : bond 0.00223 ( 39) SS BOND : angle 1.46036 ( 78) covalent geometry : bond 0.00358 (20740) covalent geometry : angle 0.65773 (28188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8826 (mmm) cc_final: 0.8470 (mmm) REVERT: A 626 MET cc_start: 0.7586 (tmm) cc_final: 0.6048 (ppp) REVERT: A 629 MET cc_start: 0.9562 (mmp) cc_final: 0.9274 (mmp) REVERT: C 373 MET cc_start: 0.9545 (pmm) cc_final: 0.9088 (pmm) REVERT: D 90 TYR cc_start: 0.9302 (m-10) cc_final: 0.8994 (m-10) REVERT: B 589 ASP cc_start: 0.9626 (m-30) cc_final: 0.9403 (m-30) REVERT: B 595 ILE cc_start: 0.9671 (mm) cc_final: 0.9298 (tt) REVERT: B 626 MET cc_start: 0.6670 (ppp) cc_final: 0.4747 (ppp) REVERT: F 154 MET cc_start: 0.8605 (mmp) cc_final: 0.8030 (mmm) REVERT: I 530 MET cc_start: 0.8201 (mmm) cc_final: 0.7990 (mmm) REVERT: I 589 ASP cc_start: 0.9469 (m-30) cc_final: 0.9211 (m-30) REVERT: I 626 MET cc_start: 0.7646 (ppp) cc_final: 0.6194 (ppp) REVERT: J 100 MET cc_start: 0.9347 (mtm) cc_final: 0.9053 (mtt) REVERT: J 150 MET cc_start: 0.7260 (pmm) cc_final: 0.6715 (tpp) REVERT: J 154 MET cc_start: 0.7942 (mmp) cc_final: 0.7715 (mmp) REVERT: J 454 LEU cc_start: 0.9638 (mt) cc_final: 0.9416 (mt) REVERT: K 90 TYR cc_start: 0.9081 (m-80) cc_final: 0.8588 (m-10) REVERT: K 100 MET cc_start: 0.9539 (mpp) cc_final: 0.8841 (mpp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3875 time to fit residues: 60.9951 Evaluate side-chains 87 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 54 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 61 optimal weight: 0.0980 chunk 81 optimal weight: 8.9990 chunk 176 optimal weight: 0.1980 chunk 194 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.032889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.026321 restraints weight = 348393.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.026993 restraints weight = 205902.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027461 restraints weight = 143264.361| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20908 Z= 0.117 Angle : 0.673 14.374 28653 Z= 0.310 Chirality : 0.048 0.407 3558 Planarity : 0.003 0.034 3384 Dihedral : 8.238 58.454 5154 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.39 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2301 helix: 0.15 (0.28), residues: 342 sheet: 0.01 (0.25), residues: 477 loop : -1.64 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 479 HIS 0.003 0.001 HIS J 105 PHE 0.010 0.001 PHE J 468 TYR 0.009 0.001 TYR C 217 ARG 0.007 0.000 ARG K 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 66) link_NAG-ASN : angle 2.79152 ( 198) link_ALPHA1-6 : bond 0.00859 ( 6) link_ALPHA1-6 : angle 1.28041 ( 18) link_BETA1-4 : bond 0.00603 ( 42) link_BETA1-4 : angle 1.77903 ( 126) link_ALPHA1-2 : bond 0.00869 ( 6) link_ALPHA1-2 : angle 3.37594 ( 18) link_ALPHA1-3 : bond 0.00901 ( 9) link_ALPHA1-3 : angle 1.67467 ( 27) hydrogen bonds : bond 0.03402 ( 437) hydrogen bonds : angle 5.14984 ( 1140) SS BOND : bond 0.00221 ( 39) SS BOND : angle 1.12447 ( 78) covalent geometry : bond 0.00248 (20740) covalent geometry : angle 0.61409 (28188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8894 (mmm) cc_final: 0.8438 (mmm) REVERT: A 626 MET cc_start: 0.7484 (tmm) cc_final: 0.6023 (ppp) REVERT: C 373 MET cc_start: 0.9513 (pmm) cc_final: 0.9061 (pmm) REVERT: D 90 TYR cc_start: 0.9293 (m-10) cc_final: 0.8962 (m-10) REVERT: B 530 MET cc_start: 0.8493 (mmm) cc_final: 0.7751 (mmm) REVERT: B 577 GLN cc_start: 0.9529 (mm110) cc_final: 0.8976 (tp40) REVERT: B 589 ASP cc_start: 0.9609 (m-30) cc_final: 0.9057 (p0) REVERT: B 595 ILE cc_start: 0.9674 (mm) cc_final: 0.9318 (tt) REVERT: B 626 MET cc_start: 0.6730 (ppp) cc_final: 0.5089 (ppp) REVERT: F 104 MET cc_start: 0.9537 (ppp) cc_final: 0.9245 (ppp) REVERT: F 154 MET cc_start: 0.8580 (mmp) cc_final: 0.8262 (mmm) REVERT: I 530 MET cc_start: 0.8482 (mmm) cc_final: 0.8149 (mmm) REVERT: I 589 ASP cc_start: 0.9428 (m-30) cc_final: 0.9166 (m-30) REVERT: I 626 MET cc_start: 0.7915 (ppp) cc_final: 0.6589 (ppp) REVERT: J 100 MET cc_start: 0.9352 (mtm) cc_final: 0.9087 (mtt) REVERT: J 104 MET cc_start: 0.9504 (ppp) cc_final: 0.9284 (ppp) REVERT: J 150 MET cc_start: 0.7116 (pmm) cc_final: 0.6617 (tpp) REVERT: J 154 MET cc_start: 0.7868 (mmp) cc_final: 0.7585 (mmp) REVERT: K 90 TYR cc_start: 0.9050 (m-80) cc_final: 0.8535 (m-10) REVERT: K 100 MET cc_start: 0.9549 (mpp) cc_final: 0.8883 (mpp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3733 time to fit residues: 60.9774 Evaluate side-chains 84 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 146 optimal weight: 30.0000 chunk 210 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 0.0170 chunk 133 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.025666 restraints weight = 353655.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.026308 restraints weight = 210682.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.026745 restraints weight = 147783.917| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20908 Z= 0.149 Angle : 0.696 14.357 28653 Z= 0.320 Chirality : 0.048 0.420 3558 Planarity : 0.003 0.033 3384 Dihedral : 8.193 57.694 5154 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.95 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2301 helix: 0.24 (0.28), residues: 342 sheet: -0.12 (0.24), residues: 504 loop : -1.67 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 479 HIS 0.004 0.001 HIS J 374 PHE 0.009 0.001 PHE J 468 TYR 0.026 0.001 TYR J 191 ARG 0.005 0.000 ARG I 633 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 66) link_NAG-ASN : angle 3.14399 ( 198) link_ALPHA1-6 : bond 0.00796 ( 6) link_ALPHA1-6 : angle 1.32826 ( 18) link_BETA1-4 : bond 0.00600 ( 42) link_BETA1-4 : angle 1.82467 ( 126) link_ALPHA1-2 : bond 0.00810 ( 6) link_ALPHA1-2 : angle 3.20604 ( 18) link_ALPHA1-3 : bond 0.00817 ( 9) link_ALPHA1-3 : angle 1.78135 ( 27) hydrogen bonds : bond 0.03366 ( 437) hydrogen bonds : angle 5.27490 ( 1140) SS BOND : bond 0.00302 ( 39) SS BOND : angle 1.35342 ( 78) covalent geometry : bond 0.00316 (20740) covalent geometry : angle 0.62613 (28188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9058 (mmm) cc_final: 0.8798 (mmm) REVERT: A 589 ASP cc_start: 0.9309 (m-30) cc_final: 0.9036 (m-30) REVERT: A 626 MET cc_start: 0.7238 (tmm) cc_final: 0.6845 (tmm) REVERT: C 373 MET cc_start: 0.9503 (pmm) cc_final: 0.9090 (pmm) REVERT: D 90 TYR cc_start: 0.9298 (m-10) cc_final: 0.9007 (m-10) REVERT: B 530 MET cc_start: 0.8479 (mmm) cc_final: 0.8085 (mmm) REVERT: B 589 ASP cc_start: 0.9622 (m-30) cc_final: 0.9413 (m-30) REVERT: B 595 ILE cc_start: 0.9692 (mm) cc_final: 0.9332 (tt) REVERT: B 626 MET cc_start: 0.6033 (ppp) cc_final: 0.4404 (ppp) REVERT: F 154 MET cc_start: 0.8596 (mmp) cc_final: 0.8051 (mmm) REVERT: G 100 LYS cc_start: 0.9615 (mmtm) cc_final: 0.9410 (tptt) REVERT: I 530 MET cc_start: 0.8550 (mmm) cc_final: 0.8196 (mmm) REVERT: I 589 ASP cc_start: 0.9447 (m-30) cc_final: 0.9215 (m-30) REVERT: I 626 MET cc_start: 0.7935 (ppp) cc_final: 0.6862 (ppp) REVERT: J 100 MET cc_start: 0.9387 (mtm) cc_final: 0.9132 (mtt) REVERT: J 150 MET cc_start: 0.7219 (pmm) cc_final: 0.6743 (tpp) REVERT: J 154 MET cc_start: 0.7786 (mmp) cc_final: 0.7144 (mmp) REVERT: K 31 ASP cc_start: 0.9587 (t0) cc_final: 0.9313 (m-30) REVERT: K 90 TYR cc_start: 0.9116 (m-80) cc_final: 0.8678 (m-10) REVERT: K 100 MET cc_start: 0.9554 (mpp) cc_final: 0.8884 (mpp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3582 time to fit residues: 56.6528 Evaluate side-chains 85 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 140 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 116 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 GLN J 474 ASN ** K 1 GLN ** 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 = 0.2986 r_free = 0.2986 target = 0.030623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.024354 restraints weight = 367988.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.024981 restraints weight = 221520.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.025404 restraints weight = 155670.138| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20908 Z= 0.212 Angle : 0.773 13.680 28653 Z= 0.364 Chirality : 0.048 0.429 3558 Planarity : 0.004 0.032 3384 Dihedral : 8.582 57.801 5154 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.21 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2301 helix: -0.10 (0.27), residues: 363 sheet: -0.44 (0.23), residues: 537 loop : -1.84 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 479 HIS 0.006 0.002 HIS C 374 PHE 0.015 0.002 PHE B 522 TYR 0.015 0.002 TYR J 191 ARG 0.009 0.001 ARG E 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 66) link_NAG-ASN : angle 3.10011 ( 198) link_ALPHA1-6 : bond 0.00756 ( 6) link_ALPHA1-6 : angle 1.31834 ( 18) link_BETA1-4 : bond 0.00552 ( 42) link_BETA1-4 : angle 1.86988 ( 126) link_ALPHA1-2 : bond 0.00587 ( 6) link_ALPHA1-2 : angle 3.14549 ( 18) link_ALPHA1-3 : bond 0.00690 ( 9) link_ALPHA1-3 : angle 1.88821 ( 27) hydrogen bonds : bond 0.03706 ( 437) hydrogen bonds : angle 5.64172 ( 1140) SS BOND : bond 0.00323 ( 39) SS BOND : angle 1.52465 ( 78) covalent geometry : bond 0.00443 (20740) covalent geometry : angle 0.71221 (28188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 589 ASP cc_start: 0.9415 (m-30) cc_final: 0.9174 (m-30) REVERT: A 626 MET cc_start: 0.7520 (tmm) cc_final: 0.7110 (tmm) REVERT: C 373 MET cc_start: 0.9535 (pmm) cc_final: 0.9257 (pmm) REVERT: B 595 ILE cc_start: 0.9712 (mm) cc_final: 0.9330 (tt) REVERT: B 626 MET cc_start: 0.6537 (ppp) cc_final: 0.5078 (ppp) REVERT: B 629 MET cc_start: 0.9583 (mmp) cc_final: 0.9345 (mmp) REVERT: F 104 MET cc_start: 0.9598 (ppp) cc_final: 0.9376 (ppp) REVERT: F 154 MET cc_start: 0.8792 (mmp) cc_final: 0.8201 (mmm) REVERT: I 589 ASP cc_start: 0.9478 (m-30) cc_final: 0.9263 (m-30) REVERT: I 626 MET cc_start: 0.8037 (ppp) cc_final: 0.7274 (ppp) REVERT: J 100 MET cc_start: 0.9374 (mtm) cc_final: 0.9136 (mtt) REVERT: J 150 MET cc_start: 0.7455 (pmm) cc_final: 0.6869 (tpp) REVERT: J 154 MET cc_start: 0.7799 (mmp) cc_final: 0.7594 (mmp) REVERT: K 31 ASP cc_start: 0.9597 (t0) cc_final: 0.9309 (m-30) REVERT: K 90 TYR cc_start: 0.9136 (m-80) cc_final: 0.8648 (m-10) REVERT: K 100 MET cc_start: 0.9529 (mpp) cc_final: 0.8839 (mpp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3412 time to fit residues: 51.3377 Evaluate side-chains 78 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 172 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 135 optimal weight: 0.0170 chunk 78 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 194 optimal weight: 0.0050 chunk 72 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 overall best weight: 4.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.030466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.024288 restraints weight = 364901.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.024896 restraints weight = 218251.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.025326 restraints weight = 152800.233| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20908 Z= 0.187 Angle : 0.731 13.472 28653 Z= 0.343 Chirality : 0.048 0.418 3558 Planarity : 0.004 0.034 3384 Dihedral : 8.586 57.857 5154 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.52 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.17), residues: 2301 helix: 0.14 (0.27), residues: 345 sheet: -0.50 (0.22), residues: 558 loop : -1.94 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 571 HIS 0.004 0.001 HIS J 374 PHE 0.013 0.002 PHE J 468 TYR 0.016 0.002 TYR J 191 ARG 0.007 0.001 ARG F 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 66) link_NAG-ASN : angle 2.87771 ( 198) link_ALPHA1-6 : bond 0.00783 ( 6) link_ALPHA1-6 : angle 1.27874 ( 18) link_BETA1-4 : bond 0.00505 ( 42) link_BETA1-4 : angle 1.70556 ( 126) link_ALPHA1-2 : bond 0.00485 ( 6) link_ALPHA1-2 : angle 3.14868 ( 18) link_ALPHA1-3 : bond 0.00815 ( 9) link_ALPHA1-3 : angle 1.77372 ( 27) hydrogen bonds : bond 0.03612 ( 437) hydrogen bonds : angle 5.60502 ( 1140) SS BOND : bond 0.00345 ( 39) SS BOND : angle 1.55049 ( 78) covalent geometry : bond 0.00390 (20740) covalent geometry : angle 0.67470 (28188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.356 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 589 ASP cc_start: 0.9389 (m-30) cc_final: 0.9149 (m-30) REVERT: A 626 MET cc_start: 0.7825 (tmm) cc_final: 0.7543 (tmm) REVERT: C 373 MET cc_start: 0.9508 (pmm) cc_final: 0.9178 (pmm) REVERT: B 530 MET cc_start: 0.9215 (mmm) cc_final: 0.8729 (mmm) REVERT: B 595 ILE cc_start: 0.9697 (mm) cc_final: 0.9340 (tt) REVERT: B 626 MET cc_start: 0.6525 (ppp) cc_final: 0.5083 (ppp) REVERT: F 104 MET cc_start: 0.9532 (ppp) cc_final: 0.9298 (ppp) REVERT: F 154 MET cc_start: 0.8740 (mmp) cc_final: 0.8260 (mmp) REVERT: H 60 ASP cc_start: 0.9732 (t0) cc_final: 0.9492 (p0) REVERT: I 589 ASP cc_start: 0.9494 (m-30) cc_final: 0.9276 (m-30) REVERT: I 626 MET cc_start: 0.8005 (ppp) cc_final: 0.6087 (ppp) REVERT: J 100 MET cc_start: 0.9392 (mtm) cc_final: 0.9154 (mtt) REVERT: J 150 MET cc_start: 0.7415 (pmm) cc_final: 0.6853 (tpp) REVERT: J 373 MET cc_start: 0.9286 (mpp) cc_final: 0.8835 (mmm) REVERT: J 454 LEU cc_start: 0.9591 (mt) cc_final: 0.9387 (mt) REVERT: K 90 TYR cc_start: 0.9158 (m-80) cc_final: 0.8634 (m-10) REVERT: K 100 MET cc_start: 0.9516 (mpp) cc_final: 0.8785 (mpp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.4448 time to fit residues: 65.6071 Evaluate side-chains 78 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 116 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 176 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 229 optimal weight: 50.0000 chunk 228 optimal weight: 7.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 650 GLN ** K 1 GLN ** 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 = 0.2970 r_free = 0.2970 target = 0.030156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.024037 restraints weight = 369737.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.024633 restraints weight = 220017.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.025056 restraints weight = 153198.496| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20908 Z= 0.176 Angle : 0.728 13.045 28653 Z= 0.341 Chirality : 0.048 0.430 3558 Planarity : 0.004 0.051 3384 Dihedral : 8.554 57.728 5154 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.82 % Favored : 90.05 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.17), residues: 2301 helix: 0.21 (0.28), residues: 345 sheet: -0.47 (0.22), residues: 540 loop : -1.92 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 479 HIS 0.004 0.001 HIS J 374 PHE 0.013 0.002 PHE J 468 TYR 0.014 0.002 TYR C 217 ARG 0.012 0.000 ARG F 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 66) link_NAG-ASN : angle 2.91711 ( 198) link_ALPHA1-6 : bond 0.00794 ( 6) link_ALPHA1-6 : angle 1.26159 ( 18) link_BETA1-4 : bond 0.00513 ( 42) link_BETA1-4 : angle 1.71531 ( 126) link_ALPHA1-2 : bond 0.00578 ( 6) link_ALPHA1-2 : angle 3.11256 ( 18) link_ALPHA1-3 : bond 0.00759 ( 9) link_ALPHA1-3 : angle 1.72493 ( 27) hydrogen bonds : bond 0.03420 ( 437) hydrogen bonds : angle 5.55288 ( 1140) SS BOND : bond 0.00273 ( 39) SS BOND : angle 1.52826 ( 78) covalent geometry : bond 0.00372 (20740) covalent geometry : angle 0.67068 (28188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 3.128 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 589 ASP cc_start: 0.9402 (m-30) cc_final: 0.9168 (m-30) REVERT: A 626 MET cc_start: 0.7802 (tmm) cc_final: 0.6610 (ppp) REVERT: C 373 MET cc_start: 0.9530 (pmm) cc_final: 0.9233 (pmm) REVERT: B 530 MET cc_start: 0.9286 (mmm) cc_final: 0.8605 (mmm) REVERT: B 595 ILE cc_start: 0.9707 (mm) cc_final: 0.9367 (tt) REVERT: B 626 MET cc_start: 0.6726 (ppp) cc_final: 0.5188 (ppp) REVERT: F 104 MET cc_start: 0.9579 (ppp) cc_final: 0.9333 (ppp) REVERT: F 154 MET cc_start: 0.8495 (mmp) cc_final: 0.7999 (mmp) REVERT: H 60 ASP cc_start: 0.9751 (t0) cc_final: 0.9531 (p0) REVERT: I 589 ASP cc_start: 0.9507 (m-30) cc_final: 0.9288 (m-30) REVERT: I 626 MET cc_start: 0.7701 (ppp) cc_final: 0.6512 (ppp) REVERT: J 150 MET cc_start: 0.7534 (pmm) cc_final: 0.7027 (tpp) REVERT: K 31 ASP cc_start: 0.9675 (t70) cc_final: 0.9436 (m-30) REVERT: K 100 MET cc_start: 0.9517 (mpp) cc_final: 0.8838 (mpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4175 time to fit residues: 60.8405 Evaluate side-chains 76 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 179 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 93 optimal weight: 0.0370 chunk 8 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 1 GLN ** 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 = 0.2863 r_free = 0.2863 target = 0.027742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.019778 restraints weight = 325801.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.020423 restraints weight = 189192.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.020896 restraints weight = 132908.061| |-----------------------------------------------------------------------------| r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.6916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20908 Z= 0.200 Angle : 0.749 12.659 28653 Z= 0.354 Chirality : 0.049 0.420 3558 Planarity : 0.004 0.040 3384 Dihedral : 8.641 57.628 5154 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.91 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.17), residues: 2301 helix: 0.18 (0.28), residues: 342 sheet: -0.55 (0.22), residues: 540 loop : -1.95 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 571 HIS 0.006 0.001 HIS C 374 PHE 0.015 0.002 PHE J 468 TYR 0.024 0.002 TYR C 435 ARG 0.005 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 66) link_NAG-ASN : angle 2.93602 ( 198) link_ALPHA1-6 : bond 0.00762 ( 6) link_ALPHA1-6 : angle 1.27101 ( 18) link_BETA1-4 : bond 0.00481 ( 42) link_BETA1-4 : angle 1.67273 ( 126) link_ALPHA1-2 : bond 0.00467 ( 6) link_ALPHA1-2 : angle 3.04357 ( 18) link_ALPHA1-3 : bond 0.00717 ( 9) link_ALPHA1-3 : angle 1.73884 ( 27) hydrogen bonds : bond 0.03623 ( 437) hydrogen bonds : angle 5.76815 ( 1140) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.50520 ( 78) covalent geometry : bond 0.00421 (20740) covalent geometry : angle 0.69336 (28188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.42 seconds wall clock time: 107 minutes 23.49 seconds (6443.49 seconds total)