Starting phenix.real_space_refine on Fri Jun 20 18:39:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7us6_26727/06_2025/7us6_26727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7us6_26727/06_2025/7us6_26727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7us6_26727/06_2025/7us6_26727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7us6_26727/06_2025/7us6_26727.map" model { file = "/net/cci-nas-00/data/ceres_data/7us6_26727/06_2025/7us6_26727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7us6_26727/06_2025/7us6_26727.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 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 124 5.16 5 C 15235 2.51 5 N 3932 2.21 5 O 4456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 167 residue(s): 1.68s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23747 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 7464 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 40, 'TRANS': 1012} Chain breaks: 8 Unresolved non-hydrogen bonds: 651 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 44, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 400 Chain: "B" Number of atoms: 7409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 7409 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 259} Link IDs: {'PTRANS': 40, 'TRANS': 1012} Chain breaks: 8 Unresolved non-hydrogen bonds: 708 Unresolved non-hydrogen angles: 900 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 16, 'TRP:plan': 2, 'ASP:plan': 48, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 431 Chain: "C" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 7430 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 249} Link IDs: {'PTRANS': 40, 'TRANS': 1012} Chain breaks: 8 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 877 Unresolved non-hydrogen dihedrals: 529 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 45, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 413 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" 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: "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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'BMA': 1, 'MAN': 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: "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: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 16.85, per 1000 atoms: 0.71 Number of scatterers: 23747 At special positions: 0 Unit cell: (144.996, 155.955, 157.641, 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 124 16.00 O 4456 8.00 N 3932 7.00 C 15235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 444 " distance=2.13 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 492 " distance=2.09 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 626 " distance=2.09 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 594 " distance=2.03 Simple disulfide: pdb=" SG CYS A 609 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 736 " distance=2.04 Simple disulfide: pdb=" SG CYS A 797 " - pdb=" SG CYS A 809 " distance=2.03 Simple disulfide: pdb=" SG CYS A 860 " - pdb=" SG CYS A 882 " distance=2.10 Simple disulfide: pdb=" SG CYS A 865 " - pdb=" SG CYS A 871 " distance=2.04 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 994 " distance=2.04 Simple disulfide: pdb=" SG CYS A1186 " - pdb=" SG CYS A1197 " distance=2.02 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1287 " distance=2.13 Simple disulfide: pdb=" SG CYS B 250 " - pdb=" SG CYS B 254 " distance=2.03 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 444 " distance=2.13 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 492 " distance=2.09 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 626 " distance=2.09 Simple disulfide: pdb=" SG CYS B 581 " - pdb=" SG CYS B 594 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 685 " - pdb=" SG CYS B 736 " distance=2.04 Simple disulfide: pdb=" SG CYS B 797 " - pdb=" SG CYS B 809 " distance=2.03 Simple disulfide: pdb=" SG CYS B 860 " - pdb=" SG CYS B 882 " distance=2.10 Simple disulfide: pdb=" SG CYS B 865 " - pdb=" SG CYS B 871 " distance=2.04 Simple disulfide: pdb=" SG CYS B 983 " - pdb=" SG CYS B 994 " distance=2.04 Simple disulfide: pdb=" SG CYS B1186 " - pdb=" SG CYS B1197 " distance=2.02 Simple disulfide: pdb=" SG CYS B1236 " - pdb=" SG CYS B1287 " distance=2.13 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 254 " distance=2.03 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 444 " distance=2.13 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 492 " distance=2.09 Simple disulfide: pdb=" SG CYS C 567 " - pdb=" SG CYS C 626 " distance=2.09 Simple disulfide: pdb=" SG CYS C 581 " - pdb=" SG CYS C 594 " distance=2.03 Simple disulfide: pdb=" SG CYS C 609 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 685 " - pdb=" SG CYS C 736 " distance=2.04 Simple disulfide: pdb=" SG CYS C 797 " - pdb=" SG CYS C 809 " distance=2.03 Simple disulfide: pdb=" SG CYS C 860 " - pdb=" SG CYS C 882 " distance=2.11 Simple disulfide: pdb=" SG CYS C 865 " - pdb=" SG CYS C 871 " distance=2.04 Simple disulfide: pdb=" SG CYS C 983 " - pdb=" SG CYS C 994 " distance=2.04 Simple disulfide: pdb=" SG CYS C1186 " - pdb=" SG CYS C1197 " distance=2.02 Simple disulfide: pdb=" SG CYS C1236 " - pdb=" SG CYS C1287 " distance=2.13 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 E 3 " - " MAN E 4 " " BMA H 1 " - " MAN H 2 " " BMA N 3 " - " MAN N 4 " " BMA Q 1 " - " MAN Q 2 " " BMA V 3 " - " MAN V 4 " " BMA Y 1 " - " MAN Y 2 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 1 " - " MAN H 3 " " BMA N 3 " - " MAN N 5 " " BMA Q 1 " - " MAN Q 3 " " BMA V 3 " - " MAN V 5 " " BMA Y 1 " - " MAN Y 3 " 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 H 1 " " 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 Q 1 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA Y 1 " " 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-ASN " NAG A1501 " - " ASN A 531 " " NAG A1502 " - " ASN A 42 " " NAG A1503 " - " ASN A 242 " " NAG A1504 " - " ASN A 448 " " NAG A1505 " - " ASN A 779 " " NAG A1506 " - " ASN A 553 " " NAG A1507 " - " ASN A 703 " " NAG A1508 " - " ASN A 818 " " NAG A1509 " - " ASN A 920 " " NAG A1510 " - " ASN A1293 " " NAG A1511 " - " ASN A 561 " " NAG A1512 " - " ASN A 404 " " NAG A1513 " - " ASN A 361 " " NAG A1514 " - " ASN A 515 " " NAG B1501 " - " ASN B 531 " " NAG B1502 " - " ASN B 42 " " NAG B1503 " - " ASN B 242 " " NAG B1504 " - " ASN B 448 " " NAG B1505 " - " ASN B 779 " " NAG B1506 " - " ASN B 553 " " NAG B1507 " - " ASN B 703 " " NAG B1508 " - " ASN B 818 " " NAG B1509 " - " ASN B 920 " " NAG B1510 " - " ASN B1293 " " NAG B1511 " - " ASN B 344 " " NAG B1512 " - " ASN B 561 " " NAG B1513 " - " ASN B 404 " " NAG B1514 " - " ASN B 361 " " NAG B1515 " - " ASN B 515 " " NAG C1501 " - " ASN C 531 " " NAG C1502 " - " ASN C 42 " " NAG C1503 " - " ASN C 242 " " NAG C1504 " - " ASN C 448 " " NAG C1505 " - " ASN C 779 " " NAG C1506 " - " ASN C 553 " " NAG C1507 " - " ASN C 703 " " NAG C1508 " - " ASN C 818 " " NAG C1509 " - " ASN C 920 " " NAG C1510 " - " ASN C1293 " " NAG C1511 " - " ASN C 561 " " NAG C1512 " - " ASN C 404 " " NAG C1513 " - " ASN C 361 " " NAG C1514 " - " ASN C 515 " " NAG D 1 " - " ASN A 249 " " NAG E 1 " - " ASN A1199 " " NAG F 1 " - " ASN A 839 " " NAG G 1 " - " ASN A 284 " " NAG I 1 " - " ASN A 724 " " NAG J 1 " - " ASN A 833 " " NAG K 1 " - " ASN A1073 " " NAG L 1 " - " ASN A 344 " " NAG M 1 " - " ASN B 249 " " NAG N 1 " - " ASN B1199 " " NAG O 1 " - " ASN B 839 " " NAG P 1 " - " ASN B 284 " " NAG R 1 " - " ASN B 724 " " NAG S 1 " - " ASN B 833 " " NAG T 1 " - " ASN B1073 " " NAG U 1 " - " ASN C 249 " " NAG V 1 " - " ASN C1199 " " NAG W 1 " - " ASN C 839 " " NAG X 1 " - " ASN C 284 " " NAG Z 1 " - " ASN C 724 " " NAG a 1 " - " ASN C 833 " " NAG b 1 " - " ASN C1073 " " NAG c 1 " - " ASN C 344 " Time building additional restraints: 7.30 Conformation dependent library (CDL) restraints added in 3.3 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 45 sheets defined 26.6% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 removed outlier: 4.150A pdb=" N ILE A 36 " --> pdb=" O HIS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 868 through 875 removed outlier: 3.662A pdb=" N LYS A 873 " --> pdb=" O PRO A 869 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 904 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 926 through 930 removed outlier: 3.519A pdb=" N LYS A 930 " --> pdb=" O PRO A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 938 No H-bonds generated for 'chain 'A' and resid 936 through 938' Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 991 through 998 Processing helix chain 'A' and resid 1009 through 1022 Processing helix chain 'A' and resid 1037 through 1050 removed outlier: 3.743A pdb=" N TYR A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1080 Processing helix chain 'A' and resid 1093 through 1118 Processing helix chain 'A' and resid 1119 through 1122 Processing helix chain 'A' and resid 1130 through 1138 Processing helix chain 'A' and resid 1139 through 1187 removed outlier: 4.867A pdb=" N ALA A1145 " --> pdb=" O PRO A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1279 No H-bonds generated for 'chain 'A' and resid 1277 through 1279' Processing helix chain 'A' and resid 1298 through 1303 Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 253 through 261 Processing helix chain 'B' and resid 485 through 495 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 868 through 875 removed outlier: 3.661A pdb=" N LYS B 873 " --> pdb=" O PRO B 869 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 904 Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 915 through 920 Processing helix chain 'B' and resid 926 through 930 removed outlier: 3.519A pdb=" N LYS B 930 " --> pdb=" O PRO B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 938 No H-bonds generated for 'chain 'B' and resid 936 through 938' Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 980 through 985 Processing helix chain 'B' and resid 991 through 998 Processing helix chain 'B' and resid 1009 through 1022 Processing helix chain 'B' and resid 1037 through 1050 removed outlier: 3.743A pdb=" N TYR B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1080 Processing helix chain 'B' and resid 1093 through 1118 Processing helix chain 'B' and resid 1119 through 1122 Processing helix chain 'B' and resid 1130 through 1138 Processing helix chain 'B' and resid 1139 through 1187 removed outlier: 4.867A pdb=" N ALA B1145 " --> pdb=" O PRO B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1279 No H-bonds generated for 'chain 'B' and resid 1277 through 1279' Processing helix chain 'B' and resid 1298 through 1303 Processing helix chain 'C' and resid 33 through 44 Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 485 through 495 Processing helix chain 'C' and resid 595 through 598 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 868 through 875 removed outlier: 3.661A pdb=" N LYS C 873 " --> pdb=" O PRO C 869 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 874 " --> pdb=" O ARG C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 904 Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 915 through 920 Processing helix chain 'C' and resid 926 through 930 removed outlier: 3.519A pdb=" N LYS C 930 " --> pdb=" O PRO C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 938 No H-bonds generated for 'chain 'C' and resid 936 through 938' Processing helix chain 'C' and resid 939 through 944 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 980 through 985 Processing helix chain 'C' and resid 991 through 998 Processing helix chain 'C' and resid 1009 through 1022 Processing helix chain 'C' and resid 1037 through 1050 removed outlier: 3.744A pdb=" N TYR C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1080 Processing helix chain 'C' and resid 1093 through 1118 Processing helix chain 'C' and resid 1119 through 1122 Processing helix chain 'C' and resid 1130 through 1138 Processing helix chain 'C' and resid 1139 through 1187 removed outlier: 4.867A pdb=" N ALA C1145 " --> pdb=" O PRO C1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1279 No H-bonds generated for 'chain 'C' and resid 1277 through 1279' Processing helix chain 'C' and resid 1298 through 1303 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU A 299 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER A 464 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL A 301 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 462 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS A 303 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 460 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP A 305 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP A 458 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN A 342 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 460 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG A 340 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR A 462 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 338 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 431 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU A 299 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER A 464 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL A 301 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 462 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS A 303 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 460 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP A 305 " --> pdb=" O TRP A 458 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP A 458 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU A 467 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR A 482 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 469 " --> pdb=" O VAL A 480 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A 480 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN A 471 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 318 removed outlier: 3.642A pdb=" N VAL A 357 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 318 removed outlier: 3.642A pdb=" N VAL A 357 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR A 356 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS A 372 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS A 399 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR A 410 " --> pdb=" O CYS A 399 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 401 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 502 through 507 removed outlier: 3.504A pdb=" N GLY A 751 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 745 " --> pdb=" O ILE A 749 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE A 749 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 765 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 515 through 519 removed outlier: 6.683A pdb=" N ASN A 515 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN A 689 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER A 517 " --> pdb=" O ASN A 689 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 730 " --> pdb=" O THR A 702 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A 720 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR A 712 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 553 through 555 removed outlier: 6.732A pdb=" N THR A 528 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR A 576 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 530 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS A 578 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 532 " --> pdb=" O HIS A 578 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 580 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 534 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LYS A 582 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 536 " --> pdb=" O LYS A 582 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 removed outlier: 4.445A pdb=" N GLY A 661 " --> pdb=" O PHE A 622 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 572 through 583 current: chain 'A' and resid 600 through 605 Processing sheet with id=AB2, first strand: chain 'A' and resid 801 through 803 Processing sheet with id=AB3, first strand: chain 'A' and resid 832 through 850 removed outlier: 6.561A pdb=" N ASN A 833 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR A1230 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 835 " --> pdb=" O THR A1228 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A1228 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR A1226 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN A 839 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY A1213 " --> pdb=" O ALA A1209 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA A1209 " --> pdb=" O GLY A1213 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A1215 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA A1207 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE A1217 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A1205 " --> pdb=" O PHE A1217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR A1219 " --> pdb=" O LEU A1203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 856 through 858 Processing sheet with id=AB5, first strand: chain 'A' and resid 1281 through 1284 Processing sheet with id=AB6, first strand: chain 'A' and resid 1253 through 1257 Processing sheet with id=AB7, first strand: chain 'B' and resid 52 through 57 Processing sheet with id=AB8, first strand: chain 'B' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU B 299 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER B 464 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL B 301 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR B 462 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS B 303 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 460 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP B 305 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP B 458 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN B 342 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 460 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 340 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR B 462 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 338 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 431 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU B 299 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER B 464 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL B 301 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR B 462 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS B 303 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 460 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP B 305 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP B 458 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU B 467 " --> pdb=" O TYR B 482 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR B 482 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 469 " --> pdb=" O VAL B 480 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 480 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN B 471 " --> pdb=" O LYS B 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 314 through 318 removed outlier: 3.643A pdb=" N VAL B 357 " --> pdb=" O ASN B 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 314 through 318 removed outlier: 3.643A pdb=" N VAL B 357 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR B 356 " --> pdb=" O CYS B 372 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS B 372 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS B 399 " --> pdb=" O TYR B 410 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR B 410 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 401 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC4, first strand: chain 'B' and resid 502 through 507 removed outlier: 3.504A pdb=" N GLY B 751 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 745 " --> pdb=" O ILE B 749 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE B 749 " --> pdb=" O ILE B 745 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS B 765 " --> pdb=" O SER B 776 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 515 through 519 removed outlier: 6.683A pdb=" N ASN B 515 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN B 689 " --> pdb=" O ASN B 515 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 517 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 730 " --> pdb=" O THR B 702 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 720 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR B 712 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 555 removed outlier: 6.732A pdb=" N THR B 528 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR B 576 " --> pdb=" O THR B 528 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 530 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS B 578 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B 532 " --> pdb=" O HIS B 578 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR B 580 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE B 534 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LYS B 582 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU B 536 " --> pdb=" O LYS B 582 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 565 through 567 removed outlier: 4.445A pdb=" N GLY B 661 " --> pdb=" O PHE B 622 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 572 through 583 current: chain 'B' and resid 600 through 605 Processing sheet with id=AC8, first strand: chain 'B' and resid 801 through 803 Processing sheet with id=AC9, first strand: chain 'B' and resid 832 through 850 removed outlier: 6.561A pdb=" N ASN B 833 " --> pdb=" O THR B1230 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR B1230 " --> pdb=" O ASN B 833 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR B 835 " --> pdb=" O THR B1228 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR B1228 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR B1226 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN B 839 " --> pdb=" O THR B1224 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY B1213 " --> pdb=" O ALA B1209 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA B1209 " --> pdb=" O GLY B1213 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B1215 " --> pdb=" O ALA B1207 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA B1207 " --> pdb=" O ILE B1215 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE B1217 " --> pdb=" O SER B1205 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B1205 " --> pdb=" O PHE B1217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR B1219 " --> pdb=" O LEU B1203 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 856 through 858 Processing sheet with id=AD2, first strand: chain 'B' and resid 1281 through 1284 Processing sheet with id=AD3, first strand: chain 'B' and resid 1253 through 1257 Processing sheet with id=AD4, first strand: chain 'C' and resid 52 through 57 Processing sheet with id=AD5, first strand: chain 'C' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU C 299 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER C 464 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL C 301 " --> pdb=" O TYR C 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR C 462 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS C 303 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 460 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP C 305 " --> pdb=" O TRP C 458 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP C 458 " --> pdb=" O TRP C 305 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C 342 " --> pdb=" O TRP C 458 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE C 460 " --> pdb=" O ARG C 340 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG C 340 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR C 462 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 338 " --> pdb=" O TYR C 462 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 431 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN C 435 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 291 through 306 removed outlier: 3.522A pdb=" N LEU C 299 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER C 464 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL C 301 " --> pdb=" O TYR C 462 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR C 462 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS C 303 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 460 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TRP C 305 " --> pdb=" O TRP C 458 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TRP C 458 " --> pdb=" O TRP C 305 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLU C 467 " --> pdb=" O TYR C 482 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR C 482 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 469 " --> pdb=" O VAL C 480 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL C 480 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN C 471 " --> pdb=" O LYS C 478 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 314 through 318 removed outlier: 3.643A pdb=" N VAL C 357 " --> pdb=" O ASN C 448 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 314 through 318 removed outlier: 3.643A pdb=" N VAL C 357 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR C 356 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N CYS C 372 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS C 399 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 410 " --> pdb=" O CYS C 399 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL C 401 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 502 through 507 removed outlier: 3.504A pdb=" N GLY C 751 " --> pdb=" O ALA C 743 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 745 " --> pdb=" O ILE C 749 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE C 749 " --> pdb=" O ILE C 745 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS C 765 " --> pdb=" O SER C 776 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 515 through 519 removed outlier: 6.683A pdb=" N ASN C 515 " --> pdb=" O ASP C 687 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN C 689 " --> pdb=" O ASN C 515 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER C 517 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C 730 " --> pdb=" O THR C 702 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU C 720 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR C 712 " --> pdb=" O LEU C 720 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 553 through 555 removed outlier: 6.733A pdb=" N THR C 528 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR C 576 " --> pdb=" O THR C 528 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 530 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS C 578 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE C 532 " --> pdb=" O HIS C 578 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR C 580 " --> pdb=" O ILE C 532 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 534 " --> pdb=" O THR C 580 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LYS C 582 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU C 536 " --> pdb=" O LYS C 582 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 565 through 567 removed outlier: 4.445A pdb=" N GLY C 661 " --> pdb=" O PHE C 622 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 572 through 583 current: chain 'C' and resid 600 through 605 Processing sheet with id=AE5, first strand: chain 'C' and resid 801 through 803 Processing sheet with id=AE6, first strand: chain 'C' and resid 832 through 850 removed outlier: 6.560A pdb=" N ASN C 833 " --> pdb=" O THR C1230 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR C1230 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C 835 " --> pdb=" O THR C1228 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C1228 " --> pdb=" O THR C 835 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR C1226 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN C 839 " --> pdb=" O THR C1224 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY C1213 " --> pdb=" O ALA C1209 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA C1209 " --> pdb=" O GLY C1213 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C1215 " --> pdb=" O ALA C1207 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALA C1207 " --> pdb=" O ILE C1215 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE C1217 " --> pdb=" O SER C1205 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C1205 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR C1219 " --> pdb=" O LEU C1203 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 856 through 858 Processing sheet with id=AE8, first strand: chain 'C' and resid 1281 through 1284 Processing sheet with id=AE9, first strand: chain 'C' and resid 1253 through 1257 1017 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.94 Time building geometry restraints manager: 8.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3846 1.31 - 1.45: 7384 1.45 - 1.59: 12805 1.59 - 1.73: 18 1.73 - 1.86: 155 Bond restraints: 24208 Sorted by residual: bond pdb=" C CYS A 865 " pdb=" O CYS A 865 " ideal model delta sigma weight residual 1.234 1.334 -0.100 1.16e-02 7.43e+03 7.36e+01 bond pdb=" C CYS C 865 " pdb=" O CYS C 865 " ideal model delta sigma weight residual 1.234 1.334 -0.099 1.16e-02 7.43e+03 7.34e+01 bond pdb=" C CYS B 865 " pdb=" O CYS B 865 " ideal model delta sigma weight residual 1.234 1.334 -0.099 1.16e-02 7.43e+03 7.34e+01 bond pdb=" C CYS C 581 " pdb=" O CYS C 581 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.19e-02 7.06e+03 2.54e+01 bond pdb=" C CYS B 581 " pdb=" O CYS B 581 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.19e-02 7.06e+03 2.51e+01 ... (remaining 24203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 32504 4.10 - 8.20: 650 8.20 - 12.30: 21 12.30 - 16.41: 6 16.41 - 20.51: 9 Bond angle restraints: 33190 Sorted by residual: angle pdb=" CG1 VAL B 349 " pdb=" CB VAL B 349 " pdb=" CG2 VAL B 349 " ideal model delta sigma weight residual 110.80 131.31 -20.51 2.20e+00 2.07e-01 8.69e+01 angle pdb=" CG1 VAL C 349 " pdb=" CB VAL C 349 " pdb=" CG2 VAL C 349 " ideal model delta sigma weight residual 110.80 131.29 -20.49 2.20e+00 2.07e-01 8.67e+01 angle pdb=" CG1 VAL A 349 " pdb=" CB VAL A 349 " pdb=" CG2 VAL A 349 " ideal model delta sigma weight residual 110.80 131.28 -20.48 2.20e+00 2.07e-01 8.67e+01 angle pdb=" CD1 LEU C 598 " pdb=" CG LEU C 598 " pdb=" CD2 LEU C 598 " ideal model delta sigma weight residual 110.80 129.53 -18.73 2.20e+00 2.07e-01 7.25e+01 angle pdb=" CD1 LEU B 598 " pdb=" CG LEU B 598 " pdb=" CD2 LEU B 598 " ideal model delta sigma weight residual 110.80 129.49 -18.69 2.20e+00 2.07e-01 7.22e+01 ... (remaining 33185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 14971 21.66 - 43.32: 392 43.32 - 64.98: 88 64.98 - 86.64: 44 86.64 - 108.30: 26 Dihedral angle restraints: 15521 sinusoidal: 6352 harmonic: 9169 Sorted by residual: dihedral pdb=" C CYS A 865 " pdb=" N CYS A 865 " pdb=" CA CYS A 865 " pdb=" CB CYS A 865 " ideal model delta harmonic sigma weight residual -122.60 -137.27 14.67 0 2.50e+00 1.60e-01 3.45e+01 dihedral pdb=" C CYS B 865 " pdb=" N CYS B 865 " pdb=" CA CYS B 865 " pdb=" CB CYS B 865 " ideal model delta harmonic sigma weight residual -122.60 -137.26 14.66 0 2.50e+00 1.60e-01 3.44e+01 dihedral pdb=" C CYS C 865 " pdb=" N CYS C 865 " pdb=" CA CYS C 865 " pdb=" CB CYS C 865 " ideal model delta harmonic sigma weight residual -122.60 -137.24 14.64 0 2.50e+00 1.60e-01 3.43e+01 ... (remaining 15518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 3855 0.165 - 0.331: 424 0.331 - 0.496: 62 0.496 - 0.662: 3 0.662 - 0.827: 6 Chirality restraints: 4350 Sorted by residual: chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.87e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.83e+02 ... (remaining 4347 not shown) Planarity restraints: 4163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.150 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" C7 NAG W 2 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.203 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.150 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" C7 NAG O 2 " 0.031 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " -0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.150 2.00e-02 2.50e+03 1.27e-01 2.01e+02 pdb=" C7 NAG F 2 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.120 2.00e-02 2.50e+03 ... (remaining 4160 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 325 2.66 - 3.22: 21547 3.22 - 3.78: 34497 3.78 - 4.34: 48565 4.34 - 4.90: 77722 Nonbonded interactions: 182656 Sorted by model distance: nonbonded pdb=" O ASN A 866 " pdb=" OD1 ASN A 866 " model vdw 2.101 3.040 nonbonded pdb=" O ASN C 866 " pdb=" OD1 ASN C 866 " model vdw 2.101 3.040 nonbonded pdb=" O ASN B 866 " pdb=" OD1 ASN B 866 " model vdw 2.102 3.040 nonbonded pdb=" NZ LYS A1249 " pdb=" OD1 ASP C1280 " model vdw 2.476 3.120 nonbonded pdb=" C ASN B 866 " pdb=" OD1 ASN B 866 " model vdw 2.487 3.270 ... (remaining 182651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 43 or (resid 44 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 49 or (resid 50 through \ 53 and (name N or name CA or name C or name O or name CB )) or resid 54 through \ 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 through 60 or (resid 61 through 234 and (name N or name CA or name C or na \ me O or name CB )) or resid 235 through 238 or (resid 239 through 240 and (name \ N or name CA or name C or name O or name CB )) or resid 241 through 258 or (resi \ d 259 and (name N or name CA or name C or name O or name CB )) or resid 260 thro \ ugh 314 or (resid 315 and (name N or name CA or name C or name O or name CB )) o \ r resid 316 through 352 or (resid 353 and (name N or name CA or name C or name O \ or name CB )) or resid 354 through 358 or (resid 359 and (name N or name CA or \ name C or name O or name CB )) or resid 360 through 362 or (resid 363 and (name \ N or name CA or name C or name O or name CB )) or resid 364 through 368 or (resi \ d 369 and (name N or name CA or name C or name O or name CB )) or resid 370 or ( \ resid 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ through 391 or (resid 392 and (name N or name CA or name C or name O or name CB \ )) or resid 393 through 405 or (resid 406 and (name N or name CA or name C or na \ me O or name CB )) or resid 407 through 473 or (resid 474 and (name N or name CA \ or name C or name O or name CB )) or resid 475 through 478 or (resid 479 and (n \ ame N or name CA or name C or name O or name CB )) or resid 480 through 495 or ( \ resid 496 through 498 and (name N or name CA or name C or name O or name CB )) o \ r resid 499 through 520 or (resid 521 and (name N or name CA or name C or name O \ or name CB )) or resid 522 through 524 or (resid 525 through 526 and (name N or \ name CA or name C or name O or name CB )) or resid 527 through 548 or (resid 54 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 550 through \ 554 or (resid 555 and (name N or name CA or name C or name O or name CB )) or re \ sid 556 through 562 or (resid 563 through 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 620 or (resid 621 and (name N or nam \ e CA or name C or name O or name CB )) or resid 622 through 731 or (resid 732 an \ d (name N or name CA or name C or name O or name CB )) or resid 733 through 757 \ or (resid 758 through 759 and (name N or name CA or name C or name O or name CB \ )) or resid 760 through 780 or (resid 781 through 796 and (name N or name CA or \ name C or name O or name CB )) or resid 797 through 821 or (resid 822 through 82 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 824 through \ 842 or (resid 843 and (name N or name CA or name C or name O or name CB )) or re \ sid 844 through 856 or (resid 857 through 858 and (name N or name CA or name C o \ r name O or name CB )) or resid 859 through 901 or (resid 902 and (name N or nam \ e CA or name C or name O or name CB )) or resid 903 through 906 or (resid 907 th \ rough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 \ through 914 or (resid 915 and (name N or name CA or name C or name O or name CB \ )) or resid 916 through 937 or (resid 938 and (name N or name CA or name C or na \ me O or name CB )) or resid 939 through 955 or (resid 956 and (name N or name CA \ or name C or name O or name CB )) or resid 957 through 978 or (resid 979 and (n \ ame N or name CA or name C or name O or name CB )) or resid 980 through 1103 or \ (resid 1104 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 05 through 1163 or (resid 1164 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1165 through 1174 or (resid 1175 and (name N or name CA or name \ C or name O or name CB )) or resid 1176 through 1188 or (resid 1189 and (name N \ or name CA or name C or name O or name CB )) or resid 1190 or (resid 1191 throu \ gh 1192 and (name N or name CA or name C or name O or name CB )) or resid 1193 t \ hrough 1204 or (resid 1205 and (name N or name CA or name C or name O or name CB \ )) or resid 1206 through 1251 or (resid 1252 and (name N or name CA or name C o \ r name O or name CB )) or resid 1253 through 1289 or (resid 1290 and (name N or \ name CA or name C or name O or name CB )) or resid 1291 through 1303 or resid 15 \ 01 through 1514)) selection = (chain 'B' and (resid 32 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 49 or (resid 50 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 246 or (re \ sid 247 through 248 and (name N or name CA or name C or name O or name CB )) or \ resid 249 through 308 or (resid 309 and (name N or name CA or name C or name O o \ r name CB )) or resid 310 through 350 or (resid 351 and (name N or name CA or na \ me C or name O or name CB )) or resid 352 through 362 or (resid 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 405 or (resid \ 406 and (name N or name CA or name C or name O or name CB )) or resid 407 throug \ h 484 or (resid 485 and (name N or name CA or name C or name O or name CB )) or \ resid 486 through 573 or (resid 574 and (name N or name CA or name C or name O o \ r name CB )) or resid 575 through 600 or (resid 601 through 602 and (name N or n \ ame CA or name C or name O or name CB )) or resid 603 through 620 or (resid 621 \ and (name N or name CA or name C or name O or name CB )) or resid 622 through 65 \ 6 or (resid 657 and (name N or name CA or name C or name O or name CB )) or resi \ d 658 through 662 or (resid 663 and (name N or name CA or name C or name O or na \ me CB )) or resid 664 through 709 or (resid 710 and (name N or name CA or name C \ or name O or name CB )) or resid 711 through 731 or (resid 732 and (name N or n \ ame CA or name C or name O or name CB )) or resid 733 through 770 or (resid 771 \ and (name N or name CA or name C or name O or name CB )) or resid 772 through 77 \ 5 or (resid 776 and (name N or name CA or name C or name O or name CB )) or resi \ d 777 through 780 or (resid 781 through 796 and (name N or name CA or name C or \ name O or name CB )) or resid 797 through 809 or (resid 810 and (name N or name \ CA or name C or name O or name CB )) or resid 811 through 842 or (resid 843 and \ (name N or name CA or name C or name O or name CB )) or resid 844 through 923 or \ (resid 924 and (name N or name CA or name C or name O or name CB )) or resid 92 \ 5 through 1008 or (resid 1009 through 1011 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1012 through 1018 or (resid 1019 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1020 through 1054 or (resid 1055 \ through 1059 and (name N or name CA or name C or name O or name CB )) or resid \ 1060 through 1102 or (resid 1103 through 1104 and (name N or name CA or name C o \ r name O or name CB )) or resid 1105 through 1106 or (resid 1107 and (name N or \ name CA or name C or name O or name CB )) or resid 1108 through 1174 or (resid 1 \ 175 and (name N or name CA or name C or name O or name CB )) or resid 1176 throu \ gh 1232 or (resid 1233 and (name N or name CA or name C or name O or name CB )) \ or resid 1234 through 1289 or (resid 1290 and (name N or name CA or name C or na \ me O or name CB )) or resid 1291 through 1303 or resid 1501 through 1514)) selection = (chain 'C' and (resid 32 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 238 or (resid 239 through 240 and \ (name N or name CA or name C or name O or name CB )) or resid 241 through 258 or \ (resid 259 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 0 through 289 or (resid 290 and (name N or name CA or name C or name O or name C \ B )) or resid 291 through 314 or (resid 315 and (name N or name CA or name C or \ name O or name CB )) or resid 316 through 350 or (resid 351 and (name N or name \ CA or name C or name O or name CB )) or resid 352 through 391 or (resid 392 and \ (name N or name CA or name C or name O or name CB )) or resid 393 through 423 or \ (resid 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 through 473 or (resid 474 and (name N or name CA or name C or name O or name C \ B )) or resid 475 through 484 or (resid 485 and (name N or name CA or name C or \ name O or name CB )) or resid 486 through 554 or (resid 555 and (name N or name \ CA or name C or name O or name CB )) or resid 556 through 573 or (resid 574 and \ (name N or name CA or name C or name O or name CB )) or resid 575 through 600 or \ (resid 601 through 602 and (name N or name CA or name C or name O or name CB )) \ or resid 603 through 638 or (resid 639 and (name N or name CA or name C or name \ O or name CB )) or resid 640 through 662 or (resid 663 and (name N or name CA o \ r name C or name O or name CB )) or resid 664 through 669 or (resid 678 and (nam \ e N or name CA or name C or name O or name CB )) or resid 679 through 754 or (re \ sid 755 and (name N or name CA or name C or name O or name CB )) or resid 756 th \ rough 763 or (resid 764 and (name N or name CA or name C or name O or name CB )) \ or resid 765 through 803 or (resid 804 and (name N or name CA or name C or name \ O or name CB )) or resid 805 through 809 or (resid 810 and (name N or name CA o \ r name C or name O or name CB )) or resid 811 through 857 or (resid 858 and (nam \ e N or name CA or name C or name O or name CB )) or resid 859 through 876 or (re \ sid 877 and (name N or name CA or name C or name O or name CB )) or resid 878 or \ (resid 879 through 881 and (name N or name CA or name C or name O or name CB )) \ or resid 882 through 914 or (resid 915 and (name N or name CA or name C or name \ O or name CB )) or resid 916 through 937 or (resid 938 and (name N or name CA o \ r name C or name O or name CB )) or resid 939 through 1008 or (resid 1009 throug \ h 1011 and (name N or name CA or name C or name O or name CB )) or resid 1012 th \ rough 1054 or (resid 1055 through 1059 and (name N or name CA or name C or name \ O or name CB )) or resid 1060 through 1127 or (resid 1128 through 1130 and (name \ N or name CA or name C or name O or name CB )) or resid 1131 or (resid 1132 thr \ ough 1133 and (name N or name CA or name C or name O or name CB )) or resid 1134 \ through 1162 or (resid 1163 through 1164 and (name N or name CA or name C or na \ me O or name CB )) or resid 1165 through 1180 or (resid 1181 and (name N or name \ CA or name C or name O or name CB )) or resid 1182 through 1191 or (resid 1192 \ and (name N or name CA or name C or name O or name CB )) or resid 1193 through 1 \ 204 or (resid 1205 and (name N or name CA or name C or name O or name CB )) or r \ esid 1206 through 1251 or (resid 1252 and (name N or name CA or name C or name O \ or name CB )) or resid 1253 through 1261 or (resid 1262 and (name N or name CA \ or name C or name O or name CB )) or resid 1263 through 1279 or (resid 1280 and \ (name N or name CA or name C or name O or name CB )) or resid 1281 through 1303 \ or resid 1501 through 1514)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'V' } ncs_group { reference = chain 'H' selection = chain 'Q' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.210 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: 1.020 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 63.160 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.015 0.134 24360 Z= 0.849 Angle : 1.533 20.507 33601 Z= 0.962 Chirality : 0.111 0.827 4350 Planarity : 0.008 0.127 4097 Dihedral : 12.014 108.301 9488 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.71 % Favored : 96.91 % Rotamer: Outliers : 0.45 % Allowed : 1.96 % Favored : 97.58 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3105 helix: 0.51 (0.17), residues: 729 sheet: 0.61 (0.18), residues: 756 loop : -0.14 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.006 TRP A 458 HIS 0.006 0.001 HIS C1202 PHE 0.017 0.003 PHE B1204 TYR 0.042 0.005 TYR B1016 ARG 0.004 0.001 ARG A1176 Details of bonding type rmsd link_NAG-ASN : bond 0.05489 ( 66) link_NAG-ASN : angle 3.67225 ( 198) link_ALPHA1-6 : bond 0.05706 ( 6) link_ALPHA1-6 : angle 3.41888 ( 18) link_BETA1-4 : bond 0.07725 ( 29) link_BETA1-4 : angle 3.21324 ( 87) link_ALPHA1-3 : bond 0.07384 ( 6) link_ALPHA1-3 : angle 3.43175 ( 18) hydrogen bonds : bond 0.19349 ( 963) hydrogen bonds : angle 7.58393 ( 2808) SS BOND : bond 0.04641 ( 45) SS BOND : angle 3.91237 ( 90) covalent geometry : bond 0.01471 (24208) covalent geometry : angle 1.48963 (33190) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 311 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 479 LYS cc_start: 0.7770 (ttpt) cc_final: 0.7450 (ttmt) REVERT: A 857 SER cc_start: 0.8585 (t) cc_final: 0.8364 (p) REVERT: A 1180 LYS cc_start: 0.7842 (tttt) cc_final: 0.7574 (ttmt) REVERT: A 1192 GLN cc_start: 0.7878 (mt0) cc_final: 0.7598 (mt0) REVERT: B 891 MET cc_start: 0.8459 (tpt) cc_final: 0.7875 (tpp) REVERT: B 1180 LYS cc_start: 0.7877 (tttt) cc_final: 0.7581 (ttmm) REVERT: C 891 MET cc_start: 0.8548 (tpt) cc_final: 0.8327 (tpp) REVERT: C 903 MET cc_start: 0.8566 (ttt) cc_final: 0.8187 (ttt) REVERT: C 1180 LYS cc_start: 0.7860 (tttt) cc_final: 0.7610 (ttpt) outliers start: 9 outliers final: 6 residues processed: 320 average time/residue: 0.3928 time to fit residues: 189.0293 Evaluate side-chains 167 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PRO Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 49 PRO Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 49 PRO Chi-restraints excluded: chain C residue 445 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.5980 chunk 238 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 246 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN A 619 HIS A 701 GLN A 999 ASN A1164 GLN B 619 HIS B 701 GLN B 999 ASN C 474 ASN C 619 HIS C 701 GLN C 999 ASN C1052 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.101247 restraints weight = 33111.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.100008 restraints weight = 51586.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.099428 restraints weight = 52868.116| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24360 Z= 0.163 Angle : 0.681 20.528 33601 Z= 0.340 Chirality : 0.047 0.269 4350 Planarity : 0.004 0.039 4097 Dihedral : 9.261 82.022 5575 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.02 % Allowed : 5.49 % Favored : 92.49 % 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 (0.14), residues: 3105 helix: 1.73 (0.19), residues: 720 sheet: 0.34 (0.17), residues: 792 loop : -0.09 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 458 HIS 0.003 0.001 HIS A 486 PHE 0.016 0.002 PHE B 447 TYR 0.025 0.001 TYR C 778 ARG 0.005 0.001 ARG A 894 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 66) link_NAG-ASN : angle 3.29773 ( 198) link_ALPHA1-6 : bond 0.00515 ( 6) link_ALPHA1-6 : angle 1.61844 ( 18) link_BETA1-4 : bond 0.00632 ( 29) link_BETA1-4 : angle 2.04997 ( 87) link_ALPHA1-3 : bond 0.01203 ( 6) link_ALPHA1-3 : angle 2.44151 ( 18) hydrogen bonds : bond 0.07155 ( 963) hydrogen bonds : angle 5.62090 ( 2808) SS BOND : bond 0.00347 ( 45) SS BOND : angle 2.45557 ( 90) covalent geometry : bond 0.00349 (24208) covalent geometry : angle 0.61081 (33190) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 771 ASN cc_start: 0.8381 (m110) cc_final: 0.7858 (m-40) REVERT: B 891 MET cc_start: 0.8446 (tpt) cc_final: 0.7786 (tpp) REVERT: C 891 MET cc_start: 0.8488 (tpt) cc_final: 0.8257 (tpp) REVERT: C 1180 LYS cc_start: 0.7635 (tttt) cc_final: 0.7377 (ttpt) outliers start: 40 outliers final: 22 residues processed: 236 average time/residue: 0.3420 time to fit residues: 130.2439 Evaluate side-chains 179 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 810 LYS Chi-restraints excluded: chain C residue 880 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 49 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 227 optimal weight: 0.0170 chunk 118 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A1052 GLN B 265 GLN C 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.113016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.101419 restraints weight = 33068.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100210 restraints weight = 51193.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.099072 restraints weight = 52124.566| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24360 Z= 0.130 Angle : 0.605 19.005 33601 Z= 0.298 Chirality : 0.045 0.339 4350 Planarity : 0.004 0.037 4097 Dihedral : 8.274 77.440 5566 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.29 % Favored : 98.62 % Rotamer: Outliers : 2.12 % Allowed : 7.36 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.70 (0.15), residues: 3105 helix: 1.99 (0.19), residues: 744 sheet: 0.34 (0.18), residues: 762 loop : -0.14 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 426 HIS 0.003 0.001 HIS B 486 PHE 0.013 0.001 PHE B 816 TYR 0.013 0.001 TYR C1016 ARG 0.003 0.000 ARG C 894 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 66) link_NAG-ASN : angle 3.04128 ( 198) link_ALPHA1-6 : bond 0.00602 ( 6) link_ALPHA1-6 : angle 1.67218 ( 18) link_BETA1-4 : bond 0.00568 ( 29) link_BETA1-4 : angle 1.54706 ( 87) link_ALPHA1-3 : bond 0.01379 ( 6) link_ALPHA1-3 : angle 1.72114 ( 18) hydrogen bonds : bond 0.05999 ( 963) hydrogen bonds : angle 5.00181 ( 2808) SS BOND : bond 0.00411 ( 45) SS BOND : angle 2.68038 ( 90) covalent geometry : bond 0.00274 (24208) covalent geometry : angle 0.53508 (33190) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6785 (t0) cc_final: 0.6577 (t70) REVERT: A 1173 ARG cc_start: 0.7376 (ttm170) cc_final: 0.7107 (ttp80) REVERT: B 236 TYR cc_start: 0.7654 (m-80) cc_final: 0.7435 (m-80) REVERT: B 771 ASN cc_start: 0.8491 (m110) cc_final: 0.8119 (m-40) REVERT: B 891 MET cc_start: 0.8400 (tpt) cc_final: 0.8033 (tpp) REVERT: B 1270 MET cc_start: 0.9023 (mtp) cc_final: 0.8760 (mtp) REVERT: C 39 PHE cc_start: 0.8211 (t80) cc_final: 0.7852 (t80) REVERT: C 516 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8387 (tttm) REVERT: C 730 ILE cc_start: 0.8220 (mm) cc_final: 0.7888 (mm) REVERT: C 1138 LEU cc_start: 0.8889 (mt) cc_final: 0.8665 (mt) outliers start: 42 outliers final: 23 residues processed: 231 average time/residue: 0.3538 time to fit residues: 129.9924 Evaluate side-chains 194 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 810 LYS Chi-restraints excluded: chain C residue 880 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 21 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 201 optimal weight: 0.0970 chunk 128 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 293 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.100289 restraints weight = 33382.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.097716 restraints weight = 53491.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.095411 restraints weight = 52389.711| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24360 Z= 0.131 Angle : 0.570 18.960 33601 Z= 0.280 Chirality : 0.045 0.326 4350 Planarity : 0.004 0.038 4097 Dihedral : 7.749 76.595 5566 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.51 % Favored : 98.39 % Rotamer: Outliers : 2.67 % Allowed : 8.26 % Favored : 89.07 % 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: 0.73 (0.15), residues: 3105 helix: 2.11 (0.19), residues: 744 sheet: 0.31 (0.18), residues: 759 loop : -0.14 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 426 HIS 0.003 0.001 HIS C 486 PHE 0.011 0.001 PHE C 447 TYR 0.014 0.001 TYR A1016 ARG 0.003 0.000 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 66) link_NAG-ASN : angle 3.04743 ( 198) link_ALPHA1-6 : bond 0.00583 ( 6) link_ALPHA1-6 : angle 1.68737 ( 18) link_BETA1-4 : bond 0.00440 ( 29) link_BETA1-4 : angle 1.53801 ( 87) link_ALPHA1-3 : bond 0.01275 ( 6) link_ALPHA1-3 : angle 2.11156 ( 18) hydrogen bonds : bond 0.05690 ( 963) hydrogen bonds : angle 4.78666 ( 2808) SS BOND : bond 0.00618 ( 45) SS BOND : angle 1.91315 ( 90) covalent geometry : bond 0.00287 (24208) covalent geometry : angle 0.50336 (33190) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 730 ILE cc_start: 0.8163 (mm) cc_final: 0.7839 (mm) REVERT: B 771 ASN cc_start: 0.8584 (m110) cc_final: 0.8258 (m-40) REVERT: B 891 MET cc_start: 0.8345 (tpt) cc_final: 0.8047 (tpp) REVERT: B 1270 MET cc_start: 0.9058 (mtp) cc_final: 0.8819 (mtp) REVERT: C 730 ILE cc_start: 0.8339 (mm) cc_final: 0.8039 (mm) outliers start: 53 outliers final: 34 residues processed: 223 average time/residue: 0.3423 time to fit residues: 122.6230 Evaluate side-chains 194 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 1164 GLN Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1214 MET Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 810 LYS Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 880 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 212 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 250 optimal weight: 0.7980 chunk 151 optimal weight: 0.0770 chunk 262 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 167 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100668 restraints weight = 33343.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.099372 restraints weight = 47247.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.098025 restraints weight = 52817.547| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24360 Z= 0.110 Angle : 0.538 18.896 33601 Z= 0.262 Chirality : 0.044 0.319 4350 Planarity : 0.004 0.040 4097 Dihedral : 7.279 74.293 5566 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.48 % Favored : 98.42 % Rotamer: Outliers : 2.37 % Allowed : 8.36 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.77 (0.15), residues: 3105 helix: 2.25 (0.19), residues: 744 sheet: 0.22 (0.18), residues: 771 loop : -0.12 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 426 HIS 0.002 0.000 HIS C 486 PHE 0.018 0.001 PHE C 39 TYR 0.011 0.001 TYR B 711 ARG 0.006 0.000 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 66) link_NAG-ASN : angle 3.03627 ( 198) link_ALPHA1-6 : bond 0.00697 ( 6) link_ALPHA1-6 : angle 1.63054 ( 18) link_BETA1-4 : bond 0.00489 ( 29) link_BETA1-4 : angle 1.41370 ( 87) link_ALPHA1-3 : bond 0.01200 ( 6) link_ALPHA1-3 : angle 1.85730 ( 18) hydrogen bonds : bond 0.05200 ( 963) hydrogen bonds : angle 4.58351 ( 2808) SS BOND : bond 0.00320 ( 45) SS BOND : angle 1.53103 ( 90) covalent geometry : bond 0.00227 (24208) covalent geometry : angle 0.47214 (33190) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 891 MET cc_start: 0.8330 (tpt) cc_final: 0.8065 (tpp) REVERT: B 1270 MET cc_start: 0.9022 (mtp) cc_final: 0.8807 (mtp) REVERT: C 730 ILE cc_start: 0.8241 (mm) cc_final: 0.7941 (mm) outliers start: 47 outliers final: 30 residues processed: 220 average time/residue: 0.3643 time to fit residues: 131.8623 Evaluate side-chains 194 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 1164 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 103 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.107373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.094255 restraints weight = 33694.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.089899 restraints weight = 55754.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.088287 restraints weight = 49945.556| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24360 Z= 0.242 Angle : 0.656 18.764 33601 Z= 0.319 Chirality : 0.047 0.344 4350 Planarity : 0.004 0.042 4097 Dihedral : 7.653 78.331 5566 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 2.67 % Allowed : 8.77 % Favored : 88.56 % 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: 0.43 (0.15), residues: 3105 helix: 1.76 (0.19), residues: 762 sheet: 0.34 (0.18), residues: 690 loop : -0.41 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 766 HIS 0.004 0.001 HIS B 486 PHE 0.019 0.002 PHE C 39 TYR 0.022 0.002 TYR B 803 ARG 0.005 0.001 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 66) link_NAG-ASN : angle 3.15575 ( 198) link_ALPHA1-6 : bond 0.00625 ( 6) link_ALPHA1-6 : angle 1.63198 ( 18) link_BETA1-4 : bond 0.00406 ( 29) link_BETA1-4 : angle 1.76523 ( 87) link_ALPHA1-3 : bond 0.01059 ( 6) link_ALPHA1-3 : angle 2.17419 ( 18) hydrogen bonds : bond 0.06909 ( 963) hydrogen bonds : angle 4.94306 ( 2808) SS BOND : bond 0.00535 ( 45) SS BOND : angle 2.19272 ( 90) covalent geometry : bond 0.00587 (24208) covalent geometry : angle 0.59239 (33190) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 603 VAL cc_start: 0.9393 (p) cc_final: 0.9184 (m) REVERT: B 730 ILE cc_start: 0.8252 (mm) cc_final: 0.7884 (mm) REVERT: B 898 MET cc_start: 0.8189 (mtm) cc_final: 0.7834 (mtt) outliers start: 53 outliers final: 44 residues processed: 205 average time/residue: 0.3121 time to fit residues: 108.4172 Evaluate side-chains 200 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 1164 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 14 optimal weight: 0.9990 chunk 256 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 59 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1052 GLN C1060 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.108359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.096195 restraints weight = 33824.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.090809 restraints weight = 56410.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.089956 restraints weight = 47377.130| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24360 Z= 0.145 Angle : 0.566 18.435 33601 Z= 0.276 Chirality : 0.045 0.326 4350 Planarity : 0.004 0.043 4097 Dihedral : 7.310 75.791 5566 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.23 % Rotamer: Outliers : 2.77 % Allowed : 9.32 % Favored : 87.91 % 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: 0.46 (0.15), residues: 3105 helix: 2.00 (0.19), residues: 747 sheet: 0.18 (0.18), residues: 720 loop : -0.40 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 426 HIS 0.002 0.001 HIS C 486 PHE 0.012 0.001 PHE B 39 TYR 0.013 0.001 TYR A1016 ARG 0.003 0.000 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 66) link_NAG-ASN : angle 3.03745 ( 198) link_ALPHA1-6 : bond 0.00761 ( 6) link_ALPHA1-6 : angle 1.60247 ( 18) link_BETA1-4 : bond 0.00425 ( 29) link_BETA1-4 : angle 1.48843 ( 87) link_ALPHA1-3 : bond 0.01095 ( 6) link_ALPHA1-3 : angle 1.90927 ( 18) hydrogen bonds : bond 0.05918 ( 963) hydrogen bonds : angle 4.71524 ( 2808) SS BOND : bond 0.00390 ( 45) SS BOND : angle 1.73086 ( 90) covalent geometry : bond 0.00331 (24208) covalent geometry : angle 0.50214 (33190) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 603 VAL cc_start: 0.9392 (p) cc_final: 0.9191 (m) REVERT: B 730 ILE cc_start: 0.8243 (mm) cc_final: 0.7875 (mm) REVERT: B 898 MET cc_start: 0.8190 (mtm) cc_final: 0.7867 (mtt) outliers start: 55 outliers final: 42 residues processed: 209 average time/residue: 0.3003 time to fit residues: 106.7721 Evaluate side-chains 204 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1164 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 124 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 chunk 246 optimal weight: 0.0170 chunk 187 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 214 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 270 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.110230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.094150 restraints weight = 33618.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.092169 restraints weight = 37808.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.092148 restraints weight = 44061.329| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24360 Z= 0.124 Angle : 0.545 18.441 33601 Z= 0.265 Chirality : 0.044 0.329 4350 Planarity : 0.004 0.043 4097 Dihedral : 7.029 73.477 5566 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Rotamer: Outliers : 2.27 % Allowed : 9.32 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.52 (0.15), residues: 3105 helix: 2.11 (0.20), residues: 747 sheet: 0.24 (0.18), residues: 717 loop : -0.40 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.002 0.001 HIS B1218 PHE 0.012 0.001 PHE B 39 TYR 0.012 0.001 TYR C1016 ARG 0.003 0.000 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 66) link_NAG-ASN : angle 3.02214 ( 198) link_ALPHA1-6 : bond 0.00848 ( 6) link_ALPHA1-6 : angle 1.56578 ( 18) link_BETA1-4 : bond 0.00436 ( 29) link_BETA1-4 : angle 1.42459 ( 87) link_ALPHA1-3 : bond 0.01084 ( 6) link_ALPHA1-3 : angle 1.82828 ( 18) hydrogen bonds : bond 0.05422 ( 963) hydrogen bonds : angle 4.55881 ( 2808) SS BOND : bond 0.00360 ( 45) SS BOND : angle 1.73867 ( 90) covalent geometry : bond 0.00272 (24208) covalent geometry : angle 0.47938 (33190) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 730 ILE cc_start: 0.8247 (mm) cc_final: 0.7879 (mm) REVERT: C 898 MET cc_start: 0.8164 (mtm) cc_final: 0.7875 (mtm) outliers start: 45 outliers final: 43 residues processed: 201 average time/residue: 0.3108 time to fit residues: 105.6533 Evaluate side-chains 202 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 810 LYS Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1164 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 295 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 158 optimal weight: 0.7980 chunk 249 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 215 optimal weight: 0.7980 chunk 252 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.111850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101768 restraints weight = 33342.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.100350 restraints weight = 53797.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098904 restraints weight = 60622.727| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24360 Z= 0.107 Angle : 0.525 18.549 33601 Z= 0.255 Chirality : 0.044 0.333 4350 Planarity : 0.004 0.044 4097 Dihedral : 6.760 70.509 5566 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.55 % Favored : 98.36 % Rotamer: Outliers : 2.12 % Allowed : 9.92 % Favored : 87.96 % 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: 0.64 (0.15), residues: 3105 helix: 2.22 (0.19), residues: 747 sheet: 0.26 (0.18), residues: 726 loop : -0.30 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 426 HIS 0.002 0.000 HIS C 486 PHE 0.012 0.001 PHE C 39 TYR 0.010 0.001 TYR C1016 ARG 0.003 0.000 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 66) link_NAG-ASN : angle 2.90696 ( 198) link_ALPHA1-6 : bond 0.00925 ( 6) link_ALPHA1-6 : angle 1.54238 ( 18) link_BETA1-4 : bond 0.00466 ( 29) link_BETA1-4 : angle 1.36261 ( 87) link_ALPHA1-3 : bond 0.01041 ( 6) link_ALPHA1-3 : angle 1.70492 ( 18) hydrogen bonds : bond 0.04994 ( 963) hydrogen bonds : angle 4.42211 ( 2808) SS BOND : bond 0.00340 ( 45) SS BOND : angle 1.59171 ( 90) covalent geometry : bond 0.00223 (24208) covalent geometry : angle 0.46240 (33190) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 730 ILE cc_start: 0.8263 (mm) cc_final: 0.7890 (mm) REVERT: C 898 MET cc_start: 0.8116 (mtm) cc_final: 0.7810 (mtm) outliers start: 42 outliers final: 35 residues processed: 200 average time/residue: 0.2986 time to fit residues: 99.6602 Evaluate side-chains 197 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 17 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 300 optimal weight: 0.5980 chunk 302 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.108475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.096260 restraints weight = 33713.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.091436 restraints weight = 53078.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.089126 restraints weight = 43816.622| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24360 Z= 0.172 Angle : 0.575 18.422 33601 Z= 0.280 Chirality : 0.045 0.349 4350 Planarity : 0.004 0.044 4097 Dihedral : 6.991 72.106 5566 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.19 % Favored : 97.71 % Rotamer: Outliers : 1.91 % Allowed : 10.18 % Favored : 87.91 % 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: 0.55 (0.15), residues: 3105 helix: 2.07 (0.20), residues: 747 sheet: 0.26 (0.19), residues: 720 loop : -0.34 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.003 0.001 HIS A1202 PHE 0.012 0.001 PHE B 622 TYR 0.015 0.001 TYR B 803 ARG 0.005 0.000 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 66) link_NAG-ASN : angle 2.90280 ( 198) link_ALPHA1-6 : bond 0.00824 ( 6) link_ALPHA1-6 : angle 1.53336 ( 18) link_BETA1-4 : bond 0.00407 ( 29) link_BETA1-4 : angle 1.54203 ( 87) link_ALPHA1-3 : bond 0.00953 ( 6) link_ALPHA1-3 : angle 1.86703 ( 18) hydrogen bonds : bond 0.05974 ( 963) hydrogen bonds : angle 4.64720 ( 2808) SS BOND : bond 0.00448 ( 45) SS BOND : angle 1.71206 ( 90) covalent geometry : bond 0.00404 (24208) covalent geometry : angle 0.51732 (33190) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 730 ILE cc_start: 0.8270 (mm) cc_final: 0.7917 (mm) outliers start: 38 outliers final: 36 residues processed: 187 average time/residue: 0.3081 time to fit residues: 97.7006 Evaluate side-chains 187 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 1034 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 739 SER Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 779 ASN Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 112 optimal weight: 0.0970 chunk 275 optimal weight: 0.1980 chunk 300 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.110766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.100664 restraints weight = 33356.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.099102 restraints weight = 52277.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.097464 restraints weight = 63213.418| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24360 Z= 0.113 Angle : 0.522 18.256 33601 Z= 0.255 Chirality : 0.044 0.343 4350 Planarity : 0.004 0.043 4097 Dihedral : 6.725 69.257 5566 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Rotamer: Outliers : 1.81 % Allowed : 10.38 % Favored : 87.81 % 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: 0.61 (0.15), residues: 3105 helix: 2.18 (0.20), residues: 747 sheet: 0.23 (0.18), residues: 753 loop : -0.32 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 426 HIS 0.002 0.001 HIS B1218 PHE 0.011 0.001 PHE B 772 TYR 0.015 0.001 TYR C 566 ARG 0.004 0.000 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 66) link_NAG-ASN : angle 2.76395 ( 198) link_ALPHA1-6 : bond 0.00897 ( 6) link_ALPHA1-6 : angle 1.53655 ( 18) link_BETA1-4 : bond 0.00448 ( 29) link_BETA1-4 : angle 1.33809 ( 87) link_ALPHA1-3 : bond 0.00992 ( 6) link_ALPHA1-3 : angle 1.65738 ( 18) hydrogen bonds : bond 0.05164 ( 963) hydrogen bonds : angle 4.45682 ( 2808) SS BOND : bond 0.00328 ( 45) SS BOND : angle 1.49249 ( 90) covalent geometry : bond 0.00242 (24208) covalent geometry : angle 0.46531 (33190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7239.23 seconds wall clock time: 128 minutes 55.79 seconds (7735.79 seconds total)