Starting phenix.real_space_refine on Sun Jun 22 19:10:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zmp_60253/06_2025/8zmp_60253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zmp_60253/06_2025/8zmp_60253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zmp_60253/06_2025/8zmp_60253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zmp_60253/06_2025/8zmp_60253.map" model { file = "/net/cci-nas-00/data/ceres_data/8zmp_60253/06_2025/8zmp_60253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zmp_60253/06_2025/8zmp_60253.cif" } resolution = 3.38 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= 0.001 sd= 0.087 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 16635 2.51 5 N 4230 2.21 5 O 5178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26175 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8308 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 3 Chain: "B" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8308 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 3 Chain: "C" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8308 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 53, 'TRANS': 1012} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 132 Unusual residues: {'EIC': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 132 Unusual residues: {'EIC': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 132 Unusual residues: {'EIC': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.86, per 1000 atoms: 0.68 Number of scatterers: 26175 At special positions: 0 Unit cell: (137.34, 143.88, 167.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5178 8.00 N 4230 7.00 C 16635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 420 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 512 " distance=2.04 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.04 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.04 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.04 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 834 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1302 " - " ASN A 145 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 358 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A1081 " " NAG A1307 " - " ASN A1117 " " NAG A1308 " - " ASN A 692 " " NAG A1309 " - " ASN A1057 " " NAG B1302 " - " ASN B 145 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 358 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B1081 " " NAG B1307 " - " ASN B1117 " " NAG B1308 " - " ASN B 692 " " NAG B1309 " - " ASN B1057 " " NAG C1302 " - " ASN C 145 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 358 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C1081 " " NAG C1307 " - " ASN C1117 " " NAG C1308 " - " ASN C 692 " " NAG C1309 " - " ASN C1057 " " NAG D 1 " - " ASN A 784 " " NAG E 1 " - " ASN A 159 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN A 228 " " NAG H 1 " - " ASN A 120 " " NAG I 1 " - " ASN A 319 " " NAG J 1 " - " ASN A 66 " " NAG K 1 " - " ASN A 270 " " NAG L 1 " - " ASN A 700 " " NAG M 1 " - " ASN B 784 " " NAG N 1 " - " ASN B 159 " " NAG O 1 " - " ASN B 110 " " NAG P 1 " - " ASN B 228 " " NAG Q 1 " - " ASN B 120 " " NAG R 1 " - " ASN B 319 " " NAG S 1 " - " ASN B 66 " " NAG T 1 " - " ASN B 270 " " NAG U 1 " - " ASN B 700 " " NAG V 1 " - " ASN C 784 " " NAG W 1 " - " ASN C 159 " " NAG X 1 " - " ASN C 110 " " NAG Y 1 " - " ASN C 228 " " NAG Z 1 " - " ASN C 120 " " NAG a 1 " - " ASN C 319 " " NAG b 1 " - " ASN C 66 " " NAG c 1 " - " ASN C 270 " " NAG d 1 " - " ASN C 700 " Time building additional restraints: 7.80 Conformation dependent library (CDL) restraints added in 3.7 seconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 54 sheets defined 22.9% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.655A pdb=" N VAL A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 358 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.369A pdb=" N ASN A 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 731 through 739 removed outlier: 4.071A pdb=" N LEU A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 738 " --> pdb=" O ASN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 766 removed outlier: 4.318A pdb=" N GLN A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 746 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 761 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.743A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'A' and resid 826 through 830 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.524A pdb=" N GLY A 872 " --> pdb=" O TRP A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 896 through 924 removed outlier: 3.675A pdb=" N TYR A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS A 904 " --> pdb=" O TYR A 900 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 948 removed outlier: 3.747A pdb=" N VAL A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 942 " --> pdb=" O ASN A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 967 Processing helix chain 'A' and resid 968 through 1016 removed outlier: 4.293A pdb=" N VAL A 974 " --> pdb=" O VAL A 970 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A1000 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.655A pdb=" N VAL B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 358 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.368A pdb=" N ASN B 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 731 through 739 removed outlier: 4.072A pdb=" N LEU B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 738 " --> pdb=" O ASN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 766 removed outlier: 4.318A pdb=" N GLN B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 746 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 809 removed outlier: 3.743A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 825 Processing helix chain 'B' and resid 826 through 830 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 849 through 867 Processing helix chain 'B' and resid 869 through 873 removed outlier: 3.524A pdb=" N GLY B 872 " --> pdb=" O TRP B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 896 through 924 removed outlier: 3.675A pdb=" N TYR B 900 " --> pdb=" O GLN B 896 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LYS B 904 " --> pdb=" O TYR B 900 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLN B 905 " --> pdb=" O GLU B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 948 removed outlier: 3.747A pdb=" N VAL B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 942 " --> pdb=" O ASN B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 967 Processing helix chain 'B' and resid 968 through 1016 removed outlier: 4.293A pdb=" N VAL B 974 " --> pdb=" O VAL B 970 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 975 " --> pdb=" O GLU B 971 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B1000 " --> pdb=" O ILE B 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.655A pdb=" N VAL C 355 " --> pdb=" O ASP C 352 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN C 358 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.369A pdb=" N ASN C 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 377 " --> pdb=" O LYS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 720 through 725 Processing helix chain 'C' and resid 731 through 739 removed outlier: 4.071A pdb=" N LEU C 735 " --> pdb=" O GLU C 731 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN C 738 " --> pdb=" O ASN C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 766 removed outlier: 4.319A pdb=" N GLN C 745 " --> pdb=" O SER C 741 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 746 " --> pdb=" O PHE C 742 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 761 " --> pdb=" O GLN C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.743A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 Processing helix chain 'C' and resid 826 through 830 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 849 through 867 Processing helix chain 'C' and resid 869 through 873 removed outlier: 3.524A pdb=" N GLY C 872 " --> pdb=" O TRP C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 896 through 924 removed outlier: 3.674A pdb=" N TYR C 900 " --> pdb=" O GLN C 896 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS C 904 " --> pdb=" O TYR C 900 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN C 905 " --> pdb=" O GLU C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 948 removed outlier: 3.747A pdb=" N VAL C 934 " --> pdb=" O LYS C 930 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 942 " --> pdb=" O ASN C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 967 Processing helix chain 'C' and resid 968 through 1016 removed outlier: 4.293A pdb=" N VAL C 974 " --> pdb=" O VAL C 970 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C1000 " --> pdb=" O ILE C 996 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.585A pdb=" N THR A 32 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 181 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU A 195 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS A 222 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 197 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR A 201 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA A 216 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 41 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 60 removed outlier: 4.344A pdb=" N ASP A 275 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.189A pdb=" N GLY A 101 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 128 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 162 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.613A pdb=" N LEU A 142 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 147 " --> pdb=" O LEU A 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 6.562A pdb=" N LYS A 312 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN A 529 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 314 " --> pdb=" O ASN A 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 535 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 346 removed outlier: 4.068A pdb=" N GLU A 342 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 387 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 511 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N CYS A 349 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 342 through 346 removed outlier: 4.068A pdb=" N GLU A 342 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 387 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 383 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 501 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA A 385 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 499 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER A 387 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 497 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 389 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR A 495 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AB2, first strand: chain 'A' and resid 552 through 553 removed outlier: 7.139A pdb=" N PHE A 552 " --> pdb=" O PHE B 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.456A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR A 679 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 651 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 684 through 686 removed outlier: 6.629A pdb=" N ALA A 684 " --> pdb=" O MET B 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 696 Processing sheet with id=AB6, first strand: chain 'A' and resid 700 through 711 removed outlier: 6.519A pdb=" N ASN A 700 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.570A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 770 through 772 removed outlier: 3.526A pdb=" N SER C 686 " --> pdb=" O MET A 771 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AC1, first strand: chain 'A' and resid 1064 through 1065 removed outlier: 3.780A pdb=" N ILE A1064 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1077 through 1080 Processing sheet with id=AC3, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.585A pdb=" N THR B 32 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN B 66 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR B 257 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 181 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 195 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS B 222 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 197 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B 201 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA B 216 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 53 through 60 removed outlier: 4.344A pdb=" N ASP B 275 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.189A pdb=" N GLY B 101 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 128 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE B 162 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.612A pdb=" N LEU B 142 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 147 " --> pdb=" O LEU B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 299 through 302 Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 316 removed outlier: 6.562A pdb=" N LYS B 312 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN B 529 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 314 " --> pdb=" O ASN B 529 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 535 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 342 through 346 removed outlier: 4.069A pdb=" N GLU B 342 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 387 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 511 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N CYS B 349 " --> pdb=" O CYS B 512 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 342 through 346 removed outlier: 4.069A pdb=" N GLU B 342 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 387 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 383 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER B 501 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 385 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 499 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 387 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 497 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 389 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR B 495 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AD3, first strand: chain 'B' and resid 552 through 553 removed outlier: 7.130A pdb=" N PHE B 552 " --> pdb=" O PHE C 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 641 through 642 removed outlier: 6.457A pdb=" N GLU B 641 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR B 679 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 651 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 684 through 686 removed outlier: 6.622A pdb=" N ALA B 684 " --> pdb=" O MET C 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 694 through 696 Processing sheet with id=AD7, first strand: chain 'B' and resid 700 through 711 removed outlier: 6.519A pdb=" N ASN B 700 " --> pdb=" O SER B1053 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.570A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE1, first strand: chain 'B' and resid 1064 through 1065 removed outlier: 3.779A pdb=" N ILE B1064 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1077 through 1080 Processing sheet with id=AE3, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.585A pdb=" N THR C 32 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 181 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 53 through 60 removed outlier: 4.344A pdb=" N ASP C 275 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.190A pdb=" N GLY C 101 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 128 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 162 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.613A pdb=" N LEU C 142 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR C 147 " --> pdb=" O LEU C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 299 through 302 Processing sheet with id=AE8, first strand: chain 'C' and resid 312 through 316 removed outlier: 6.562A pdb=" N LYS C 312 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN C 529 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 314 " --> pdb=" O ASN C 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 535 " --> pdb=" O PHE C 528 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 342 through 346 removed outlier: 4.068A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 511 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N CYS C 349 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 342 through 346 removed outlier: 4.068A pdb=" N GLU C 342 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 387 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL C 383 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER C 501 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA C 385 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 499 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER C 387 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 497 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 389 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR C 495 " --> pdb=" O VAL C 389 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AF3, first strand: chain 'C' and resid 641 through 642 removed outlier: 6.456A pdb=" N GLU C 641 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N THR C 679 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 651 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 694 through 696 Processing sheet with id=AF5, first strand: chain 'C' and resid 700 through 711 removed outlier: 6.518A pdb=" N ASN C 700 " --> pdb=" O SER C1053 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.570A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AF8, first strand: chain 'C' and resid 1064 through 1065 removed outlier: 3.780A pdb=" N ILE C1064 " --> pdb=" O TYR C1071 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1077 through 1080 908 hydrogen bonds defined for protein. 2508 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: 14.08 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4227 1.30 - 1.43: 7583 1.43 - 1.57: 14770 1.57 - 1.70: 0 1.70 - 1.83: 174 Bond restraints: 26754 Sorted by residual: bond pdb=" CA LEU C 210 " pdb=" C LEU C 210 " ideal model delta sigma weight residual 1.522 1.446 0.077 1.08e-02 8.57e+03 5.02e+01 bond pdb=" CA ALA A 128 " pdb=" C ALA A 128 " ideal model delta sigma weight residual 1.520 1.438 0.082 1.16e-02 7.43e+03 5.02e+01 bond pdb=" CA LEU A 210 " pdb=" C LEU A 210 " ideal model delta sigma weight residual 1.522 1.446 0.077 1.08e-02 8.57e+03 5.02e+01 bond pdb=" CA LEU B 210 " pdb=" C LEU B 210 " ideal model delta sigma weight residual 1.522 1.446 0.076 1.08e-02 8.57e+03 5.02e+01 bond pdb=" CA ALA B 128 " pdb=" C ALA B 128 " ideal model delta sigma weight residual 1.520 1.438 0.082 1.16e-02 7.43e+03 5.01e+01 ... (remaining 26749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 35434 1.91 - 3.82: 743 3.82 - 5.73: 132 5.73 - 7.64: 27 7.64 - 9.55: 33 Bond angle restraints: 36369 Sorted by residual: angle pdb=" N ASN A 159 " pdb=" CA ASN A 159 " pdb=" C ASN A 159 " ideal model delta sigma weight residual 109.96 119.21 -9.25 1.50e+00 4.44e-01 3.80e+01 angle pdb=" N ASN C 159 " pdb=" CA ASN C 159 " pdb=" C ASN C 159 " ideal model delta sigma weight residual 109.96 119.19 -9.23 1.50e+00 4.44e-01 3.79e+01 angle pdb=" N ASN B 159 " pdb=" CA ASN B 159 " pdb=" C ASN B 159 " ideal model delta sigma weight residual 109.96 119.17 -9.21 1.50e+00 4.44e-01 3.77e+01 angle pdb=" N ILE B 153 " pdb=" CA ILE B 153 " pdb=" C ILE B 153 " ideal model delta sigma weight residual 112.96 106.92 6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" N ILE A 153 " pdb=" CA ILE A 153 " pdb=" C ILE A 153 " ideal model delta sigma weight residual 112.96 106.93 6.03 1.00e+00 1.00e+00 3.63e+01 ... (remaining 36364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 15597 23.90 - 47.80: 1232 47.80 - 71.70: 181 71.70 - 95.60: 18 95.60 - 119.49: 48 Dihedral angle restraints: 17076 sinusoidal: 7776 harmonic: 9300 Sorted by residual: dihedral pdb=" CB CYS A 726 " pdb=" SG CYS A 726 " pdb=" SG CYS A 732 " pdb=" CB CYS A 732 " ideal model delta sinusoidal sigma weight residual -86.00 -148.77 62.77 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS B 726 " pdb=" SG CYS B 726 " pdb=" SG CYS B 732 " pdb=" CB CYS B 732 " ideal model delta sinusoidal sigma weight residual -86.00 -148.74 62.74 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS C 726 " pdb=" SG CYS C 726 " pdb=" SG CYS C 732 " pdb=" CB CYS C 732 " ideal model delta sinusoidal sigma weight residual -86.00 -148.74 62.74 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 17073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4089 0.098 - 0.197: 240 0.197 - 0.295: 12 0.295 - 0.394: 3 0.394 - 0.492: 3 Chirality restraints: 4347 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 159 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 159 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 159 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 4344 not shown) Planarity restraints: 4665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 206 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C ALA B 206 " 0.052 2.00e-02 2.50e+03 pdb=" O ALA B 206 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA B 207 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 206 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ALA A 206 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA A 206 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 207 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 206 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C ALA C 206 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA C 206 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 207 " -0.017 2.00e-02 2.50e+03 ... (remaining 4662 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4502 2.77 - 3.30: 23517 3.30 - 3.83: 41095 3.83 - 4.37: 47427 4.37 - 4.90: 84970 Nonbonded interactions: 201511 Sorted by model distance: nonbonded pdb=" OH TYR C 42 " pdb=" O HIS C 59 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR B 42 " pdb=" O HIS B 59 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 42 " pdb=" O HIS A 59 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 592 " pdb=" OE1 GLU B 594 " model vdw 2.239 3.040 nonbonded pdb=" OG SER A 592 " pdb=" OE1 GLU A 594 " model vdw 2.239 3.040 ... (remaining 201506 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'W' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 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: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 67.640 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.005 0.083 26883 Z= 0.337 Angle : 0.737 9.552 36714 Z= 0.394 Chirality : 0.049 0.492 4347 Planarity : 0.004 0.040 4614 Dihedral : 16.900 119.495 10962 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.41 % Allowed : 20.24 % Favored : 74.35 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3174 helix: 0.60 (0.21), residues: 678 sheet: 0.23 (0.20), residues: 642 loop : -1.96 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 246 HIS 0.001 0.000 HIS C1066 PHE 0.010 0.001 PHE C 154 TYR 0.009 0.001 TYR B1050 ARG 0.001 0.000 ARG B 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 51) link_NAG-ASN : angle 3.11064 ( 153) link_BETA1-4 : bond 0.01114 ( 33) link_BETA1-4 : angle 3.03324 ( 99) link_ALPHA1-3 : bond 0.00115 ( 3) link_ALPHA1-3 : angle 2.06071 ( 9) hydrogen bonds : bond 0.20692 ( 899) hydrogen bonds : angle 7.21657 ( 2508) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.23375 ( 84) covalent geometry : bond 0.00485 (26754) covalent geometry : angle 0.69147 (36369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 225 time to evaluate : 2.853 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: A 23 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5520 (m-10) REVERT: A 25 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6880 (p0) REVERT: A 94 GLU cc_start: 0.7213 (pt0) cc_final: 0.6796 (pt0) REVERT: A 297 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7371 (p0) REVERT: A 377 ASP cc_start: 0.8442 (m-30) cc_final: 0.8204 (m-30) REVERT: A 413 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8876 (mt) REVERT: A 519 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.8003 (t0) REVERT: A 641 GLU cc_start: 0.7826 (mp0) cc_final: 0.7495 (mm-30) REVERT: A 657 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8726 (mm) REVERT: A 731 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7834 (mt-10) REVERT: A 793 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7441 (pp) REVERT: A 975 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.6444 (mm-40) REVERT: B 25 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.6892 (p0) REVERT: B 73 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6186 (p90) REVERT: B 131 PHE cc_start: 0.8062 (m-10) cc_final: 0.7740 (m-80) REVERT: B 138 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: B 413 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8911 (mt) REVERT: B 519 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8004 (t0) REVERT: B 641 GLU cc_start: 0.8016 (mp0) cc_final: 0.7773 (mm-30) REVERT: B 657 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 793 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7735 (pp) REVERT: B 975 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6876 (mm-40) REVERT: B 1012 MET cc_start: 0.8915 (tpp) cc_final: 0.8685 (ttm) REVERT: C 23 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5829 (m-10) REVERT: C 25 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6863 (p0) REVERT: C 94 GLU cc_start: 0.7247 (pt0) cc_final: 0.6485 (pt0) REVERT: C 131 PHE cc_start: 0.8196 (m-10) cc_final: 0.7948 (m-10) REVERT: C 138 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: C 232 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8230 (p90) REVERT: C 297 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7721 (p0) REVERT: C 413 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8829 (mt) REVERT: C 519 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8089 (t0) REVERT: C 641 GLU cc_start: 0.7870 (mp0) cc_final: 0.7650 (mm-30) REVERT: C 657 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8539 (mm) REVERT: C 731 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7853 (mt-10) REVERT: C 793 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7537 (pp) REVERT: C 926 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7921 (p) REVERT: C 975 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7745 (mm-40) REVERT: C 1012 MET cc_start: 0.9014 (tpp) cc_final: 0.8710 (ttm) outliers start: 150 outliers final: 106 residues processed: 348 average time/residue: 0.3297 time to fit residues: 192.1973 Evaluate side-chains 332 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 199 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 770 GLN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 975 GLN Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 657 ILE Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 975 GLN Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 657 ILE Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 770 GLN Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 952 ASN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 975 GLN Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 128 optimal weight: 0.0980 chunk 249 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 819 GLN ** A 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 819 GLN B 938 ASN C 480 ASN C 550 GLN C 819 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099246 restraints weight = 39757.635| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.73 r_work: 0.3013 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26883 Z= 0.153 Angle : 0.679 9.037 36714 Z= 0.315 Chirality : 0.048 0.347 4347 Planarity : 0.004 0.044 4614 Dihedral : 12.374 101.514 5504 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.53 % Allowed : 18.51 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3174 helix: 0.80 (0.20), residues: 705 sheet: 0.56 (0.20), residues: 678 loop : -1.90 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 424 HIS 0.003 0.001 HIS C 38 PHE 0.018 0.001 PHE B1093 TYR 0.021 0.001 TYR A1050 ARG 0.004 0.000 ARG A 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 51) link_NAG-ASN : angle 3.32458 ( 153) link_BETA1-4 : bond 0.01037 ( 33) link_BETA1-4 : angle 3.01519 ( 99) link_ALPHA1-3 : bond 0.00514 ( 3) link_ALPHA1-3 : angle 3.91385 ( 9) hydrogen bonds : bond 0.04444 ( 899) hydrogen bonds : angle 5.31948 ( 2508) SS BOND : bond 0.00375 ( 42) SS BOND : angle 1.21396 ( 84) covalent geometry : bond 0.00359 (26754) covalent geometry : angle 0.62171 (36369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 200 time to evaluate : 2.819 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: A 23 PHE cc_start: 0.5913 (OUTLIER) cc_final: 0.5709 (m-10) REVERT: A 25 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6966 (p0) REVERT: A 94 GLU cc_start: 0.7372 (pt0) cc_final: 0.6529 (pt0) REVERT: A 413 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8818 (mt) REVERT: A 519 ASP cc_start: 0.8428 (t0) cc_final: 0.8130 (t0) REVERT: A 641 GLU cc_start: 0.7945 (mp0) cc_final: 0.7619 (mm-30) REVERT: A 793 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7468 (pp) REVERT: B 73 PHE cc_start: 0.6457 (OUTLIER) cc_final: 0.6117 (p90) REVERT: B 138 PHE cc_start: 0.8437 (m-80) cc_final: 0.7947 (m-80) REVERT: B 413 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8944 (mt) REVERT: B 793 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7781 (pp) REVERT: B 827 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7511 (mt) REVERT: B 933 ASP cc_start: 0.8907 (m-30) cc_final: 0.8628 (t0) REVERT: C 23 PHE cc_start: 0.6323 (OUTLIER) cc_final: 0.5776 (m-10) REVERT: C 25 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6903 (p0) REVERT: C 94 GLU cc_start: 0.7124 (pt0) cc_final: 0.6432 (pt0) REVERT: C 232 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8532 (p90) REVERT: C 413 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8837 (mt) REVERT: C 519 ASP cc_start: 0.8581 (t0) cc_final: 0.8258 (t0) REVERT: C 731 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8202 (mt-10) REVERT: C 793 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7412 (pp) outliers start: 181 outliers final: 122 residues processed: 357 average time/residue: 0.3180 time to fit residues: 190.7100 Evaluate side-chains 323 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 188 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 952 ASN Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 827 ILE Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 512 CYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 550 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 222 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 250 optimal weight: 0.9990 chunk 289 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 306 optimal weight: 0.9980 chunk 308 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 938 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100109 restraints weight = 39980.318| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.77 r_work: 0.3006 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26883 Z= 0.133 Angle : 0.645 8.873 36714 Z= 0.299 Chirality : 0.046 0.351 4347 Planarity : 0.004 0.037 4614 Dihedral : 10.329 84.293 5438 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.92 % Allowed : 19.34 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3174 helix: 0.91 (0.20), residues: 720 sheet: 0.54 (0.20), residues: 687 loop : -1.78 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 424 HIS 0.003 0.001 HIS C 38 PHE 0.012 0.001 PHE C1104 TYR 0.019 0.001 TYR A1050 ARG 0.004 0.000 ARG C 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 51) link_NAG-ASN : angle 3.27859 ( 153) link_BETA1-4 : bond 0.01120 ( 33) link_BETA1-4 : angle 3.08501 ( 99) link_ALPHA1-3 : bond 0.00924 ( 3) link_ALPHA1-3 : angle 3.64651 ( 9) hydrogen bonds : bond 0.04113 ( 899) hydrogen bonds : angle 4.95919 ( 2508) SS BOND : bond 0.00458 ( 42) SS BOND : angle 1.11648 ( 84) covalent geometry : bond 0.00308 (26754) covalent geometry : angle 0.58569 (36369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 195 time to evaluate : 3.205 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 25 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6866 (p0) REVERT: A 94 GLU cc_start: 0.7638 (pt0) cc_final: 0.6737 (pt0) REVERT: A 413 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8835 (mt) REVERT: A 432 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9050 (p) REVERT: A 519 ASP cc_start: 0.8500 (t0) cc_final: 0.8147 (t0) REVERT: A 641 GLU cc_start: 0.7956 (mp0) cc_final: 0.7637 (mm-30) REVERT: A 793 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7389 (pp) REVERT: B 73 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6159 (p90) REVERT: B 138 PHE cc_start: 0.8373 (m-80) cc_final: 0.7855 (m-80) REVERT: B 413 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8872 (mt) REVERT: B 415 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8645 (t0) REVERT: B 432 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9017 (p) REVERT: B 641 GLU cc_start: 0.8130 (mp0) cc_final: 0.7858 (mm-30) REVERT: B 793 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7714 (pp) REVERT: B 933 ASP cc_start: 0.8912 (m-30) cc_final: 0.8622 (t0) REVERT: C 23 PHE cc_start: 0.6310 (OUTLIER) cc_final: 0.5796 (m-10) REVERT: C 25 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6957 (p0) REVERT: C 94 GLU cc_start: 0.7144 (pt0) cc_final: 0.6585 (pt0) REVERT: C 232 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8558 (p90) REVERT: C 413 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8828 (mt) REVERT: C 432 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9039 (p) REVERT: C 519 ASP cc_start: 0.8620 (t0) cc_final: 0.8258 (t0) REVERT: C 793 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7416 (pp) outliers start: 164 outliers final: 118 residues processed: 342 average time/residue: 0.3671 time to fit residues: 212.1557 Evaluate side-chains 312 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 179 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1033 MET Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 512 CYS Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 129 optimal weight: 0.0870 chunk 184 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 237 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 288 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 938 ASN ** C 550 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 = 0.3682 r_free = 0.3682 target = 0.132548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100368 restraints weight = 40237.467| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.87 r_work: 0.3017 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26883 Z= 0.121 Angle : 0.635 8.767 36714 Z= 0.293 Chirality : 0.046 0.353 4347 Planarity : 0.004 0.037 4614 Dihedral : 9.694 59.658 5423 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.06 % Allowed : 19.41 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3174 helix: 1.01 (0.20), residues: 723 sheet: 0.51 (0.20), residues: 717 loop : -1.81 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 424 HIS 0.003 0.001 HIS B 38 PHE 0.022 0.001 PHE C 630 TYR 0.018 0.001 TYR A1050 ARG 0.002 0.000 ARG C 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 51) link_NAG-ASN : angle 3.27021 ( 153) link_BETA1-4 : bond 0.01131 ( 33) link_BETA1-4 : angle 3.06664 ( 99) link_ALPHA1-3 : bond 0.01254 ( 3) link_ALPHA1-3 : angle 2.95765 ( 9) hydrogen bonds : bond 0.03824 ( 899) hydrogen bonds : angle 4.78409 ( 2508) SS BOND : bond 0.00358 ( 42) SS BOND : angle 1.04680 ( 84) covalent geometry : bond 0.00278 (26754) covalent geometry : angle 0.57544 (36369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 188 time to evaluate : 3.037 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 25 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6829 (p0) REVERT: A 94 GLU cc_start: 0.7657 (pt0) cc_final: 0.6807 (pt0) REVERT: A 136 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8311 (t0) REVERT: A 413 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8848 (mt) REVERT: A 432 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9061 (p) REVERT: A 519 ASP cc_start: 0.8545 (t0) cc_final: 0.8207 (t0) REVERT: A 641 GLU cc_start: 0.7920 (mp0) cc_final: 0.7639 (mm-30) REVERT: A 793 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7387 (pp) REVERT: B 73 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.6071 (p90) REVERT: B 138 PHE cc_start: 0.8396 (m-80) cc_final: 0.8068 (m-10) REVERT: B 413 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8859 (mt) REVERT: B 415 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8622 (t0) REVERT: B 432 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9021 (p) REVERT: B 793 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7631 (pp) REVERT: B 933 ASP cc_start: 0.8929 (m-30) cc_final: 0.8646 (t0) REVERT: C 23 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.5790 (m-10) REVERT: C 25 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7032 (p0) REVERT: C 94 GLU cc_start: 0.7102 (pt0) cc_final: 0.6548 (pt0) REVERT: C 232 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8563 (p90) REVERT: C 432 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9038 (p) REVERT: C 519 ASP cc_start: 0.8574 (t0) cc_final: 0.8206 (t0) REVERT: C 793 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7409 (pp) REVERT: C 926 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7931 (p) outliers start: 168 outliers final: 122 residues processed: 337 average time/residue: 0.3203 time to fit residues: 181.6347 Evaluate side-chains 315 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 177 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 512 CYS Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 56 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 249 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 196 optimal weight: 0.0170 chunk 271 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 938 ASN ** C 550 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 = 0.3669 r_free = 0.3669 target = 0.131615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099279 restraints weight = 40130.832| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.89 r_work: 0.2997 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26883 Z= 0.134 Angle : 0.633 8.574 36714 Z= 0.296 Chirality : 0.047 0.353 4347 Planarity : 0.004 0.035 4614 Dihedral : 9.192 57.644 5411 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.53 % Allowed : 19.26 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3174 helix: 1.03 (0.20), residues: 723 sheet: 0.45 (0.20), residues: 714 loop : -1.74 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 424 HIS 0.003 0.001 HIS A 38 PHE 0.020 0.001 PHE A 630 TYR 0.019 0.001 TYR A1050 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 51) link_NAG-ASN : angle 3.25128 ( 153) link_BETA1-4 : bond 0.01156 ( 33) link_BETA1-4 : angle 3.09029 ( 99) link_ALPHA1-3 : bond 0.01178 ( 3) link_ALPHA1-3 : angle 2.06301 ( 9) hydrogen bonds : bond 0.03956 ( 899) hydrogen bonds : angle 4.68342 ( 2508) SS BOND : bond 0.00369 ( 42) SS BOND : angle 1.14422 ( 84) covalent geometry : bond 0.00318 (26754) covalent geometry : angle 0.57438 (36369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 183 time to evaluate : 2.910 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 25 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6878 (p0) REVERT: A 94 GLU cc_start: 0.7694 (pt0) cc_final: 0.6876 (pt0) REVERT: A 136 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8335 (t0) REVERT: A 185 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: A 413 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8832 (mt) REVERT: A 415 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8732 (t0) REVERT: A 432 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9097 (p) REVERT: A 519 ASP cc_start: 0.8541 (t0) cc_final: 0.8205 (t0) REVERT: A 641 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: A 793 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7664 (pp) REVERT: B 94 GLU cc_start: 0.7256 (pt0) cc_final: 0.7019 (pt0) REVERT: B 138 PHE cc_start: 0.8432 (m-80) cc_final: 0.7968 (m-80) REVERT: B 152 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: B 415 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8663 (t0) REVERT: B 432 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9012 (p) REVERT: B 464 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8454 (p0) REVERT: B 641 GLU cc_start: 0.8189 (mp0) cc_final: 0.7884 (mm-30) REVERT: B 793 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7635 (pp) REVERT: B 933 ASP cc_start: 0.8945 (m-30) cc_final: 0.8689 (t0) REVERT: C 25 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7032 (p0) REVERT: C 138 PHE cc_start: 0.8464 (m-80) cc_final: 0.8219 (m-80) REVERT: C 232 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8554 (p90) REVERT: C 432 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9032 (p) REVERT: C 519 ASP cc_start: 0.8582 (t0) cc_final: 0.8211 (t0) REVERT: C 710 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8656 (mtp) REVERT: C 793 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7381 (pp) REVERT: C 926 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7948 (p) REVERT: C 933 ASP cc_start: 0.8984 (m-30) cc_final: 0.8678 (m-30) outliers start: 181 outliers final: 133 residues processed: 344 average time/residue: 0.3178 time to fit residues: 184.8930 Evaluate side-chains 328 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 176 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 512 CYS Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 74 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 ASN B 480 ASN B 938 ASN ** C 550 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 = 0.3639 r_free = 0.3639 target = 0.129238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097434 restraints weight = 40179.243| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.78 r_work: 0.2970 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26883 Z= 0.174 Angle : 0.665 10.358 36714 Z= 0.315 Chirality : 0.047 0.354 4347 Planarity : 0.004 0.035 4614 Dihedral : 9.070 59.182 5403 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 6.24 % Allowed : 20.24 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 3174 helix: 0.86 (0.20), residues: 732 sheet: 0.45 (0.20), residues: 732 loop : -1.74 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 424 HIS 0.005 0.001 HIS C 38 PHE 0.018 0.001 PHE A 630 TYR 0.020 0.001 TYR A1050 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 51) link_NAG-ASN : angle 3.27771 ( 153) link_BETA1-4 : bond 0.01138 ( 33) link_BETA1-4 : angle 3.15883 ( 99) link_ALPHA1-3 : bond 0.00626 ( 3) link_ALPHA1-3 : angle 1.77036 ( 9) hydrogen bonds : bond 0.04489 ( 899) hydrogen bonds : angle 4.77880 ( 2508) SS BOND : bond 0.00397 ( 42) SS BOND : angle 1.41218 ( 84) covalent geometry : bond 0.00424 (26754) covalent geometry : angle 0.60674 (36369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 174 time to evaluate : 3.084 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 25 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6883 (p0) REVERT: A 94 GLU cc_start: 0.7674 (pt0) cc_final: 0.6804 (pt0) REVERT: A 136 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8329 (t0) REVERT: A 413 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8722 (mp) REVERT: A 415 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8808 (t0) REVERT: A 432 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.9184 (p) REVERT: A 519 ASP cc_start: 0.8674 (t0) cc_final: 0.8314 (t0) REVERT: A 641 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7893 (mm-30) REVERT: A 793 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7689 (pp) REVERT: B 138 PHE cc_start: 0.8522 (m-80) cc_final: 0.8049 (m-80) REVERT: B 152 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: B 265 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9171 (mt) REVERT: B 415 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8799 (t0) REVERT: B 600 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: B 641 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: B 685 ASP cc_start: 0.8380 (t0) cc_final: 0.8163 (t0) REVERT: B 793 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7702 (pp) REVERT: B 933 ASP cc_start: 0.9133 (m-30) cc_final: 0.8905 (t0) REVERT: C 23 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.5913 (m-10) REVERT: C 25 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7001 (p0) REVERT: C 232 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8648 (p90) REVERT: C 432 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9026 (p) REVERT: C 519 ASP cc_start: 0.8746 (t0) cc_final: 0.8402 (t0) REVERT: C 641 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: C 710 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8794 (mtp) REVERT: C 793 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7480 (pp) REVERT: C 869 TRP cc_start: 0.6743 (p90) cc_final: 0.6134 (p-90) outliers start: 173 outliers final: 128 residues processed: 329 average time/residue: 0.3376 time to fit residues: 187.7782 Evaluate side-chains 318 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 170 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 81 optimal weight: 5.9990 chunk 44 optimal weight: 0.0000 chunk 78 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 254 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 310 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 304 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 938 ASN ** C 550 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 = 0.3666 r_free = 0.3666 target = 0.131515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098835 restraints weight = 40130.533| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.79 r_work: 0.2991 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26883 Z= 0.119 Angle : 0.628 9.175 36714 Z= 0.295 Chirality : 0.046 0.354 4347 Planarity : 0.004 0.036 4614 Dihedral : 8.861 57.075 5399 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.63 % Allowed : 20.82 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3174 helix: 1.00 (0.20), residues: 729 sheet: 0.54 (0.20), residues: 714 loop : -1.70 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.004 0.001 HIS C 38 PHE 0.017 0.001 PHE A 630 TYR 0.019 0.001 TYR B1050 ARG 0.001 0.000 ARG C1002 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 51) link_NAG-ASN : angle 3.25930 ( 153) link_BETA1-4 : bond 0.01194 ( 33) link_BETA1-4 : angle 3.16449 ( 99) link_ALPHA1-3 : bond 0.00601 ( 3) link_ALPHA1-3 : angle 1.80199 ( 9) hydrogen bonds : bond 0.03894 ( 899) hydrogen bonds : angle 4.61911 ( 2508) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.12067 ( 84) covalent geometry : bond 0.00277 (26754) covalent geometry : angle 0.56804 (36369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 178 time to evaluate : 3.093 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 25 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6071 (p0) REVERT: A 94 GLU cc_start: 0.7572 (pt0) cc_final: 0.6778 (pt0) REVERT: A 136 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8351 (t0) REVERT: A 413 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8799 (mt) REVERT: A 432 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9147 (p) REVERT: A 519 ASP cc_start: 0.8510 (t0) cc_final: 0.8164 (t0) REVERT: A 641 GLU cc_start: 0.7993 (mp0) cc_final: 0.7643 (mm-30) REVERT: A 793 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7731 (pp) REVERT: A 933 ASP cc_start: 0.8824 (m-30) cc_final: 0.8281 (m-30) REVERT: B 138 PHE cc_start: 0.8426 (m-80) cc_final: 0.7961 (m-80) REVERT: B 152 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: B 265 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9116 (mt) REVERT: B 415 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8625 (t0) REVERT: B 464 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8490 (p0) REVERT: B 933 ASP cc_start: 0.8949 (m-30) cc_final: 0.8698 (t0) REVERT: C 23 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.5865 (m-10) REVERT: C 25 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7070 (p0) REVERT: C 232 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8562 (p90) REVERT: C 432 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9021 (p) REVERT: C 464 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8547 (p0) REVERT: C 519 ASP cc_start: 0.8625 (t0) cc_final: 0.8263 (t0) REVERT: C 793 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7396 (pp) REVERT: C 926 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7899 (p) REVERT: C 933 ASP cc_start: 0.8968 (m-30) cc_final: 0.8622 (m-30) outliers start: 156 outliers final: 121 residues processed: 320 average time/residue: 0.3447 time to fit residues: 186.6370 Evaluate side-chains 307 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 170 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 139 PHE Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 832 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 150 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 294 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 46 optimal weight: 0.0020 chunk 228 optimal weight: 0.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 938 ASN ** C 550 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 = 0.3615 r_free = 0.3615 target = 0.127013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095520 restraints weight = 40029.433| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.74 r_work: 0.2949 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26883 Z= 0.211 Angle : 0.697 11.153 36714 Z= 0.333 Chirality : 0.048 0.357 4347 Planarity : 0.004 0.035 4614 Dihedral : 8.929 56.705 5393 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.99 % Allowed : 20.71 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3174 helix: 0.82 (0.20), residues: 729 sheet: 0.53 (0.20), residues: 723 loop : -1.78 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 424 HIS 0.006 0.001 HIS C 38 PHE 0.019 0.001 PHE C 630 TYR 0.021 0.001 TYR C1050 ARG 0.003 0.000 ARG C 396 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 51) link_NAG-ASN : angle 3.29772 ( 153) link_BETA1-4 : bond 0.01143 ( 33) link_BETA1-4 : angle 3.24170 ( 99) link_ALPHA1-3 : bond 0.00403 ( 3) link_ALPHA1-3 : angle 1.85682 ( 9) hydrogen bonds : bond 0.04788 ( 899) hydrogen bonds : angle 4.79397 ( 2508) SS BOND : bond 0.00487 ( 42) SS BOND : angle 1.61614 ( 84) covalent geometry : bond 0.00517 (26754) covalent geometry : angle 0.63945 (36369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 169 time to evaluate : 2.804 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 25 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6070 (p0) REVERT: A 94 GLU cc_start: 0.7679 (pt0) cc_final: 0.6797 (pt0) REVERT: A 136 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8347 (t0) REVERT: A 413 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 432 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9162 (p) REVERT: A 519 ASP cc_start: 0.8662 (t0) cc_final: 0.8299 (t0) REVERT: A 793 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7931 (pp) REVERT: B 138 PHE cc_start: 0.8526 (m-80) cc_final: 0.8027 (m-80) REVERT: B 152 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: B 201 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8762 (t80) REVERT: B 265 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9155 (mt) REVERT: B 415 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8806 (t0) REVERT: B 464 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8538 (p0) REVERT: B 933 ASP cc_start: 0.9165 (m-30) cc_final: 0.8938 (t0) REVERT: C 23 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.5889 (m-10) REVERT: C 25 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7037 (p0) REVERT: C 136 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8459 (t0) REVERT: C 232 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8645 (p90) REVERT: C 265 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9372 (mt) REVERT: C 266 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8397 (tttm) REVERT: C 432 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9064 (p) REVERT: C 464 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8589 (p0) REVERT: C 519 ASP cc_start: 0.8781 (t0) cc_final: 0.8402 (t0) REVERT: C 710 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8795 (mtp) REVERT: C 793 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7528 (pp) REVERT: C 869 TRP cc_start: 0.6553 (p90) cc_final: 0.5948 (p-90) REVERT: C 926 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8072 (p) outliers start: 166 outliers final: 124 residues processed: 319 average time/residue: 0.3192 time to fit residues: 171.5639 Evaluate side-chains 312 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 167 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 751 SER Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 166 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 246 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 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 = 0.3656 r_free = 0.3656 target = 0.130954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.097935 restraints weight = 40557.082| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.92 r_work: 0.2958 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26883 Z= 0.142 Angle : 0.650 9.829 36714 Z= 0.307 Chirality : 0.047 0.354 4347 Planarity : 0.004 0.039 4614 Dihedral : 8.711 57.804 5387 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.52 % Allowed : 21.18 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3174 helix: 0.94 (0.20), residues: 729 sheet: 0.54 (0.20), residues: 723 loop : -1.76 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 424 HIS 0.004 0.001 HIS C 38 PHE 0.018 0.001 PHE C 630 TYR 0.019 0.001 TYR A1050 ARG 0.002 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 51) link_NAG-ASN : angle 3.26851 ( 153) link_BETA1-4 : bond 0.01215 ( 33) link_BETA1-4 : angle 3.25083 ( 99) link_ALPHA1-3 : bond 0.00472 ( 3) link_ALPHA1-3 : angle 1.79016 ( 9) hydrogen bonds : bond 0.04214 ( 899) hydrogen bonds : angle 4.66907 ( 2508) SS BOND : bond 0.00401 ( 42) SS BOND : angle 1.26297 ( 84) covalent geometry : bond 0.00340 (26754) covalent geometry : angle 0.59011 (36369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 170 time to evaluate : 3.283 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 25 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.5981 (p0) REVERT: A 94 GLU cc_start: 0.7520 (pt0) cc_final: 0.6605 (pt0) REVERT: A 136 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8329 (t0) REVERT: A 415 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8726 (t0) REVERT: A 432 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9147 (p) REVERT: A 519 ASP cc_start: 0.8522 (t0) cc_final: 0.8168 (t0) REVERT: A 641 GLU cc_start: 0.8080 (mp0) cc_final: 0.7765 (mm-30) REVERT: A 793 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7749 (pp) REVERT: A 933 ASP cc_start: 0.8842 (m-30) cc_final: 0.8266 (m-30) REVERT: B 136 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 138 PHE cc_start: 0.8490 (m-80) cc_final: 0.7851 (m-80) REVERT: B 152 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: B 265 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9114 (mt) REVERT: B 415 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8630 (t0) REVERT: B 464 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8508 (p0) REVERT: B 600 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: B 793 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7656 (pp) REVERT: B 933 ASP cc_start: 0.8962 (m-30) cc_final: 0.8724 (t0) REVERT: C 23 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.5816 (m-10) REVERT: C 25 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7013 (p0) REVERT: C 136 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8471 (t0) REVERT: C 232 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8556 (p90) REVERT: C 432 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.8989 (p) REVERT: C 464 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8521 (p0) REVERT: C 519 ASP cc_start: 0.8657 (t0) cc_final: 0.8294 (t0) REVERT: C 547 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: C 710 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8667 (mtp) REVERT: C 793 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7511 (pp) REVERT: C 869 TRP cc_start: 0.6445 (p90) cc_final: 0.5874 (p-90) REVERT: C 926 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7929 (p) outliers start: 153 outliers final: 121 residues processed: 306 average time/residue: 0.4160 time to fit residues: 218.3862 Evaluate side-chains 309 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 166 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 547 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 157 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 259 optimal weight: 0.5980 chunk 136 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 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 = 0.3684 r_free = 0.3684 target = 0.132748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100626 restraints weight = 39949.791| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.78 r_work: 0.3025 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26883 Z= 0.108 Angle : 0.616 9.515 36714 Z= 0.290 Chirality : 0.046 0.354 4347 Planarity : 0.004 0.037 4614 Dihedral : 8.339 57.541 5383 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.44 % Allowed : 22.08 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 3174 helix: 1.27 (0.21), residues: 711 sheet: 0.65 (0.20), residues: 705 loop : -1.67 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 246 HIS 0.003 0.001 HIS B 38 PHE 0.019 0.001 PHE A 800 TYR 0.019 0.001 TYR B1050 ARG 0.002 0.000 ARG C1002 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 51) link_NAG-ASN : angle 3.19467 ( 153) link_BETA1-4 : bond 0.01221 ( 33) link_BETA1-4 : angle 3.18508 ( 99) link_ALPHA1-3 : bond 0.00482 ( 3) link_ALPHA1-3 : angle 1.77001 ( 9) hydrogen bonds : bond 0.03516 ( 899) hydrogen bonds : angle 4.49005 ( 2508) SS BOND : bond 0.00385 ( 42) SS BOND : angle 0.95909 ( 84) covalent geometry : bond 0.00247 (26754) covalent geometry : angle 0.55673 (36369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 179 time to evaluate : 5.108 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 25 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6023 (p0) REVERT: A 94 GLU cc_start: 0.7471 (pt0) cc_final: 0.6678 (pt0) REVERT: A 136 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8417 (t0) REVERT: A 432 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9130 (p) REVERT: A 519 ASP cc_start: 0.8533 (t0) cc_final: 0.8202 (t0) REVERT: A 641 GLU cc_start: 0.8000 (mp0) cc_final: 0.7648 (mm-30) REVERT: A 926 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7902 (p) REVERT: A 933 ASP cc_start: 0.8804 (m-30) cc_final: 0.8257 (m-30) REVERT: B 136 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8382 (t0) REVERT: B 138 PHE cc_start: 0.8383 (m-80) cc_final: 0.7998 (m-10) REVERT: B 152 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: B 265 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9098 (mt) REVERT: B 464 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8569 (p0) REVERT: B 793 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7662 (pp) REVERT: C 23 PHE cc_start: 0.6332 (OUTLIER) cc_final: 0.5793 (m-10) REVERT: C 25 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7053 (p0) REVERT: C 136 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8463 (t0) REVERT: C 232 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8583 (p90) REVERT: C 432 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9062 (p) REVERT: C 464 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8515 (p0) REVERT: C 519 ASP cc_start: 0.8614 (t0) cc_final: 0.8227 (t0) REVERT: C 869 TRP cc_start: 0.6348 (p90) cc_final: 0.5799 (p-90) REVERT: C 926 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7978 (p) REVERT: C 933 ASP cc_start: 0.8930 (m-30) cc_final: 0.8578 (m-30) outliers start: 123 outliers final: 97 residues processed: 289 average time/residue: 0.4737 time to fit residues: 231.1635 Evaluate side-chains 283 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 170 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 732 CYS Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 368 TYR Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 732 CYS Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 892 ILE Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1081 ASN Chi-restraints excluded: chain C residue 23 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 158 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 324 CYS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 368 TYR Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 512 CYS Chi-restraints excluded: chain C residue 517 SER Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 547 GLN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 732 CYS Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 926 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1077 VAL Chi-restraints excluded: chain C residue 1081 ASN Chi-restraints excluded: chain C residue 1089 GLN Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 180 optimal weight: 0.2980 chunk 43 optimal weight: 0.0980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 177 optimal weight: 0.0370 chunk 245 optimal weight: 0.3980 chunk 316 optimal weight: 4.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 819 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 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 = 0.3691 r_free = 0.3691 target = 0.133378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101340 restraints weight = 40122.780| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.87 r_work: 0.3038 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26883 Z= 0.106 Angle : 0.613 9.483 36714 Z= 0.290 Chirality : 0.046 0.353 4347 Planarity : 0.004 0.037 4614 Dihedral : 8.125 56.634 5374 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.44 % Allowed : 22.08 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3174 helix: 1.34 (0.21), residues: 711 sheet: 0.71 (0.20), residues: 687 loop : -1.65 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.003 0.001 HIS B 38 PHE 0.018 0.001 PHE C 630 TYR 0.018 0.001 TYR B1050 ARG 0.001 0.000 ARG C 748 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 51) link_NAG-ASN : angle 3.14031 ( 153) link_BETA1-4 : bond 0.01199 ( 33) link_BETA1-4 : angle 3.16126 ( 99) link_ALPHA1-3 : bond 0.00440 ( 3) link_ALPHA1-3 : angle 1.76095 ( 9) hydrogen bonds : bond 0.03409 ( 899) hydrogen bonds : angle 4.43019 ( 2508) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.07063 ( 84) covalent geometry : bond 0.00243 (26754) covalent geometry : angle 0.55447 (36369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12443.10 seconds wall clock time: 220 minutes 35.54 seconds (13235.54 seconds total)