Starting phenix.real_space_refine on Sat Jul 4 22:48:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7us6_26727/07_2026/7us6_26727.cif Found real_map, /net/cci-nas-00/data/ceres_data/7us6_26727/07_2026/7us6_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_26727/07_2026/7us6_26727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7us6_26727/07_2026/7us6_26727.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7us6_26727/07_2026/7us6_26727.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7us6_26727/07_2026/7us6_26727.cif" model { file = "/net/cci-nas-00/data/ceres_data/7us6_26727/07_2026/7us6_26727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7us6_26727/07_2026/7us6_26727.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'HIS:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 18, 'GLU:plan': 23, 'ARG:plan': 5, 'ASP:plan': 44, 'GLN:plan1': 12, 'TYR:plan': 3} 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: {'HIS:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 16, 'GLU:plan': 24, 'ARG:plan': 5, 'ASP:plan': 48, 'GLN:plan1': 14, 'TYR:plan': 4, 'PHE:plan': 1} 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: {'HIS:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 17, 'GLU:plan': 24, 'ARG:plan': 5, 'ASP:plan': 45, 'GLN:plan1': 11, 'TYR:plan': 4, 'PHE:plan': 1} 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 14 Time building chain proxies: 6.14, per 1000 atoms: 0.26 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: 2.66 Conformation dependent library (CDL) restraints added in 1.1 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: 0.93 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: 6.30 Time building geometry restraints manager: 3.26 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 - 17.75: 12831 17.75 - 35.50: 366 35.50 - 53.24: 71 53.24 - 70.99: 35 70.99 - 88.74: 7 Dihedral angle restraints: 13310 sinusoidal: 4141 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 13307 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 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 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 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: 15.030 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: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.040 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 9.614 88.741 7277 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG A1176 TYR 0.042 0.005 TYR B1016 PHE 0.017 0.003 PHE B1204 TRP 0.024 0.006 TRP A 458 HIS 0.006 0.001 HIS C1202 Details of bonding type rmsd/Z covalent geometry : bond 0.01471 / 0.82 (24208) covalent geometry : angle 1.48963 / 0.96 (33190) SS BOND : bond 0.04641 / 3.11 ( 45) SS BOND : angle 3.91237 / 3.10 ( 90) hydrogen bonds : bond 0.19349 / 13.02 ( 963) hydrogen bonds : angle 7.58393 / 5.25 ( 2808) link_ALPHA1-3 : bond 0.07384 / 4.47 ( 6) link_ALPHA1-3 : angle 3.43175 / 2.37 ( 18) link_ALPHA1-6 : bond 0.05706 / 3.46 ( 6) link_ALPHA1-6 : angle 3.41888 / 2.34 ( 18) link_BETA1-4 : bond 0.07725 / 5.70 ( 29) link_BETA1-4 : angle 3.21324 / 2.57 ( 87) link_NAG-ASN : bond 0.05489 / 3.89 ( 66) link_NAG-ASN : angle 3.67225 / 2.80 ( 198) *********************** 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 : 0.924 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: 0.7874 (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: 0.1903 time to fit residues: 92.0675 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 : 0.925 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.113737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.101770 restraints weight = 33158.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.101206 restraints weight = 48391.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.098224 restraints weight = 46931.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.096103 restraints weight = 38876.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.096323 restraints weight = 40922.957| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24360 Z= 0.163 Angle : 0.675 21.419 33601 Z= 0.337 Chirality : 0.046 0.244 4350 Planarity : 0.004 0.040 4097 Dihedral : 4.738 43.438 3364 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3105 helix: 1.71 (0.19), residues: 720 sheet: 0.33 (0.17), residues: 792 loop : -0.10 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 894 TYR 0.025 0.001 TYR C 778 PHE 0.016 0.002 PHE B 447 TRP 0.010 0.001 TRP C 458 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (24208) covalent geometry : angle 0.61115 / 0.32 (33190) SS BOND : bond 0.00471 / 0.32 ( 45) SS BOND : angle 2.36056 / 1.85 ( 90) hydrogen bonds : bond 0.07021 / 4.72 ( 963) hydrogen bonds : angle 5.58065 / 3.88 ( 2808) link_ALPHA1-3 : bond 0.00608 / 0.37 ( 6) link_ALPHA1-3 : angle 1.94903 / 1.38 ( 18) link_ALPHA1-6 : bond 0.00791 / 0.48 ( 6) link_ALPHA1-6 : angle 1.46699 / 0.97 ( 18) link_BETA1-4 : bond 0.00584 / 0.42 ( 29) link_BETA1-4 : angle 1.88697 / 1.51 ( 87) link_NAG-ASN : bond 0.00722 / 0.55 ( 66) link_NAG-ASN : angle 3.15766 / 2.17 ( 198) *********************** 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 250 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.885 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: 0.8392 (m110) cc_final: 0.7878 (m-40) REVERT: B 891 MET cc_start: 0.8455 (tpt) cc_final: 0.7808 (tpp) REVERT: B 1180 LYS cc_start: 0.7822 (tttt) cc_final: 0.7612 (ttmm) REVERT: C 891 MET cc_start: 0.8497 (tpt) cc_final: 0.8267 (tpp) REVERT: C 1180 LYS cc_start: 0.7580 (tttt) cc_final: 0.7319 (ttpt) outliers start: 40 outliers final: 21 residues processed: 237 average time/residue: 0.1618 time to fit residues: 61.7790 Evaluate side-chains 178 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 103 optimal weight: 0.0040 chunk 83 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 266 optimal weight: 0.0870 overall best weight: 1.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 527 HIS A1052 GLN B 265 GLN C 265 GLN C1052 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.110309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.098135 restraints weight = 33587.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.097041 restraints weight = 54018.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.093135 restraints weight = 53734.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.091735 restraints weight = 47836.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.091852 restraints weight = 50013.109| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24360 Z= 0.184 Angle : 0.651 19.842 33601 Z= 0.321 Chirality : 0.045 0.336 4350 Planarity : 0.004 0.039 4097 Dihedral : 4.653 44.344 3355 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.35 % Favored : 98.55 % Rotamer: Outliers : 2.27 % Allowed : 7.30 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3105 helix: 1.80 (0.19), residues: 744 sheet: 0.34 (0.18), residues: 762 loop : -0.23 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 894 TYR 0.018 0.001 TYR B1016 PHE 0.013 0.002 PHE A 447 TRP 0.007 0.001 TRP C 458 HIS 0.005 0.001 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (24208) covalent geometry : angle 0.58005 / 0.30 (33190) SS BOND : bond 0.00498 / 0.35 ( 45) SS BOND : angle 3.06530 / 2.31 ( 90) hydrogen bonds : bond 0.06705 / 4.49 ( 963) hydrogen bonds : angle 5.13964 / 3.57 ( 2808) link_ALPHA1-3 : bond 0.00714 / 0.44 ( 6) link_ALPHA1-3 : angle 1.44567 / 0.97 ( 18) link_ALPHA1-6 : bond 0.00631 / 0.38 ( 6) link_ALPHA1-6 : angle 1.33003 / 0.89 ( 18) link_BETA1-4 : bond 0.00526 / 0.38 ( 29) link_BETA1-4 : angle 1.52610 / 1.18 ( 87) link_NAG-ASN : bond 0.00743 / 0.57 ( 66) link_NAG-ASN : angle 3.15243 / 2.17 ( 198) *********************** 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 226 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.894 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: 0.6977 (t0) cc_final: 0.6753 (t70) REVERT: A 1173 ARG cc_start: 0.7490 (ttm170) cc_final: 0.7192 (ttp80) REVERT: B 771 ASN cc_start: 0.8587 (m110) cc_final: 0.8138 (m-40) REVERT: B 891 MET cc_start: 0.8371 (tpt) cc_final: 0.7716 (tpp) REVERT: B 1270 MET cc_start: 0.9107 (mtp) cc_final: 0.8865 (mtp) REVERT: C 1180 LYS cc_start: 0.7532 (tttt) cc_final: 0.7258 (ttmm) outliers start: 45 outliers final: 28 residues processed: 213 average time/residue: 0.1667 time to fit residues: 56.5618 Evaluate side-chains 180 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL 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 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 1222 LEU 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 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 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 806 ILE 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 207 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 273 optimal weight: 0.8980 chunk 241 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.098909 restraints weight = 33481.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.097713 restraints weight = 57560.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.094294 restraints weight = 54244.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.092959 restraints weight = 40675.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.093221 restraints weight = 46987.548| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24360 Z= 0.138 Angle : 0.572 19.008 33601 Z= 0.283 Chirality : 0.044 0.317 4350 Planarity : 0.004 0.041 4097 Dihedral : 4.457 45.479 3355 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Rotamer: Outliers : 2.17 % Allowed : 8.31 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3105 helix: 1.97 (0.19), residues: 744 sheet: 0.26 (0.18), residues: 762 loop : -0.24 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1168 TYR 0.013 0.001 TYR A1016 PHE 0.014 0.001 PHE C 39 TRP 0.005 0.001 TRP C 426 HIS 0.003 0.001 HIS B1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (24208) covalent geometry : angle 0.50593 / 0.27 (33190) SS BOND : bond 0.00444 / 0.30 ( 45) SS BOND : angle 2.17551 / 1.62 ( 90) hydrogen bonds : bond 0.05841 / 3.92 ( 963) hydrogen bonds : angle 4.82278 / 3.37 ( 2808) link_ALPHA1-3 : bond 0.00598 / 0.36 ( 6) link_ALPHA1-3 : angle 1.47318 / 0.99 ( 18) link_ALPHA1-6 : bond 0.00613 / 0.37 ( 6) link_ALPHA1-6 : angle 1.39071 / 0.95 ( 18) link_BETA1-4 : bond 0.00432 / 0.31 ( 29) link_BETA1-4 : angle 1.34532 / 1.03 ( 87) link_NAG-ASN : bond 0.00653 / 0.49 ( 66) link_NAG-ASN : angle 3.03511 / 2.09 ( 198) *********************** 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 221 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 1.470 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 1168 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7231 (mtm110) REVERT: B 891 MET cc_start: 0.8340 (tpt) cc_final: 0.8053 (tpp) REVERT: B 1137 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7647 (mtp85) REVERT: B 1270 MET cc_start: 0.9080 (mtp) cc_final: 0.8867 (mtp) outliers start: 43 outliers final: 27 residues processed: 213 average time/residue: 0.1606 time to fit residues: 55.3371 Evaluate side-chains 175 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 679 VAL Chi-restraints excluded: chain A residue 779 ASN Chi-restraints excluded: chain A residue 803 TYR Chi-restraints excluded: chain A residue 1164 GLN Chi-restraints excluded: chain A residue 1222 LEU 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 445 ILE Chi-restraints excluded: chain B residue 603 VAL 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 B residue 1019 SER 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 880 SER Chi-restraints excluded: chain C residue 1164 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 195 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1052 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.098402 restraints weight = 33459.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.093215 restraints weight = 52909.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.091501 restraints weight = 45985.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.091375 restraints weight = 47520.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.091387 restraints weight = 45868.027| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24360 Z= 0.185 Angle : 0.601 18.878 33601 Z= 0.294 Chirality : 0.045 0.336 4350 Planarity : 0.004 0.040 4097 Dihedral : 4.542 45.988 3355 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.77 % Favored : 98.13 % Rotamer: Outliers : 2.57 % Allowed : 8.51 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3105 helix: 1.74 (0.19), residues: 768 sheet: 0.23 (0.18), residues: 732 loop : -0.39 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 894 TYR 0.016 0.001 TYR A1016 PHE 0.018 0.001 PHE C 39 TRP 0.007 0.001 TRP B 766 HIS 0.004 0.001 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (24208) covalent geometry : angle 0.54075 / 0.28 (33190) SS BOND : bond 0.00425 / 0.30 ( 45) SS BOND : angle 1.91436 / 1.49 ( 90) hydrogen bonds : bond 0.06381 / 4.27 ( 963) hydrogen bonds : angle 4.85188 / 3.38 ( 2808) link_ALPHA1-3 : bond 0.00641 / 0.38 ( 6) link_ALPHA1-3 : angle 1.49466 / 1.00 ( 18) link_ALPHA1-6 : bond 0.00554 / 0.33 ( 6) link_ALPHA1-6 : angle 1.38841 / 0.94 ( 18) link_BETA1-4 : bond 0.00403 / 0.29 ( 29) link_BETA1-4 : angle 1.47282 / 1.12 ( 87) link_NAG-ASN : bond 0.00621 / 0.47 ( 66) link_NAG-ASN : angle 3.03630 / 2.11 ( 198) *********************** 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 217 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.918 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 1168 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7081 (mtm110) REVERT: B 891 MET cc_start: 0.8326 (tpt) cc_final: 0.7758 (tpp) REVERT: B 1137 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7639 (mtp85) outliers start: 51 outliers final: 36 residues processed: 206 average time/residue: 0.1549 time to fit residues: 52.3596 Evaluate side-chains 192 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 518 VAL 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 803 TYR 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 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 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 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 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 880 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 122 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 78 optimal weight: 0.0470 chunk 208 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 177 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1052 GLN C1052 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.111418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.101028 restraints weight = 33390.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.099899 restraints weight = 55558.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098411 restraints weight = 59783.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.097827 restraints weight = 67740.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.097860 restraints weight = 52348.780| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3082 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= 0.107 Angle : 0.530 18.801 33601 Z= 0.261 Chirality : 0.043 0.317 4350 Planarity : 0.004 0.041 4097 Dihedral : 4.270 45.622 3355 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.23 % Rotamer: Outliers : 2.22 % Allowed : 9.02 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 3105 helix: 2.10 (0.19), residues: 747 sheet: 0.07 (0.18), residues: 780 loop : -0.27 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 296 TYR 0.010 0.001 TYR B 430 PHE 0.021 0.001 PHE B 39 TRP 0.007 0.001 TRP A 426 HIS 0.002 0.000 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (24208) covalent geometry : angle 0.46944 / 0.25 (33190) SS BOND : bond 0.00356 / 0.23 ( 45) SS BOND : angle 1.47529 / 1.11 ( 90) hydrogen bonds : bond 0.05290 / 3.56 ( 963) hydrogen bonds : angle 4.59059 / 3.21 ( 2808) link_ALPHA1-3 : bond 0.00649 / 0.40 ( 6) link_ALPHA1-3 : angle 1.40776 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00585 / 0.35 ( 6) link_ALPHA1-6 : angle 1.40216 / 0.95 ( 18) link_BETA1-4 : bond 0.00410 / 0.29 ( 29) link_BETA1-4 : angle 1.24322 / 0.95 ( 87) link_NAG-ASN : bond 0.00606 / 0.46 ( 66) link_NAG-ASN : angle 2.94231 / 2.04 ( 198) *********************** 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 220 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.802 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 1168 ARG cc_start: 0.7463 (mtt90) cc_final: 0.7251 (mtm110) REVERT: B 730 ILE cc_start: 0.8239 (mm) cc_final: 0.7943 (mm) REVERT: B 891 MET cc_start: 0.8247 (tpt) cc_final: 0.7989 (tpp) REVERT: B 1137 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7584 (mtp85) outliers start: 44 outliers final: 34 residues processed: 211 average time/residue: 0.1432 time to fit residues: 49.3090 Evaluate side-chains 198 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 679 VAL Chi-restraints excluded: chain A residue 779 ASN 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 1164 GLN 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 387 ASP 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 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 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 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 810 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 205 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 225 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.110839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.098677 restraints weight = 33463.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.097615 restraints weight = 53144.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.093207 restraints weight = 55139.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.092584 restraints weight = 47589.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.092654 restraints weight = 44623.126| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3205 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 : 0.527 19.018 33601 Z= 0.257 Chirality : 0.043 0.335 4350 Planarity : 0.004 0.041 4097 Dihedral : 4.161 45.461 3355 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.48 % Favored : 98.42 % Rotamer: Outliers : 2.52 % Allowed : 9.17 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3105 helix: 2.19 (0.20), residues: 747 sheet: 0.11 (0.18), residues: 771 loop : -0.28 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 894 TYR 0.011 0.001 TYR A1016 PHE 0.011 0.001 PHE B 39 TRP 0.007 0.001 TRP A 426 HIS 0.002 0.000 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (24208) covalent geometry : angle 0.46742 / 0.24 (33190) SS BOND : bond 0.00357 / 0.24 ( 45) SS BOND : angle 1.52304 / 1.15 ( 90) hydrogen bonds : bond 0.05193 / 3.48 ( 963) hydrogen bonds : angle 4.49285 / 3.14 ( 2808) link_ALPHA1-3 : bond 0.00628 / 0.39 ( 6) link_ALPHA1-3 : angle 1.41286 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00559 / 0.34 ( 6) link_ALPHA1-6 : angle 1.42021 / 0.96 ( 18) link_BETA1-4 : bond 0.00400 / 0.29 ( 29) link_BETA1-4 : angle 1.28466 / 0.98 ( 87) link_NAG-ASN : bond 0.00583 / 0.44 ( 66) link_NAG-ASN : angle 2.88159 / 1.99 ( 198) *********************** 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 219 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.843 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 913 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8681 (pp) REVERT: A 1277 THR cc_start: 0.9109 (t) cc_final: 0.8831 (p) REVERT: B 387 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8027 (t70) REVERT: B 891 MET cc_start: 0.8242 (tpt) cc_final: 0.8017 (tpp) REVERT: B 913 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8562 (pp) REVERT: B 1137 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7609 (mtp85) REVERT: B 1277 THR cc_start: 0.9110 (t) cc_final: 0.8792 (p) outliers start: 50 outliers final: 37 residues processed: 206 average time/residue: 0.1380 time to fit residues: 47.4762 Evaluate side-chains 203 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 317 PHE 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 803 TYR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 913 LEU 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 356 THR Chi-restraints excluded: chain B residue 387 ASP 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 913 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 317 PHE 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 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 1034 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 223 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.107666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.094801 restraints weight = 33735.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.090248 restraints weight = 55925.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.087967 restraints weight = 41786.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.087949 restraints weight = 45794.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.088133 restraints weight = 42289.068| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24360 Z= 0.201 Angle : 0.613 18.915 33601 Z= 0.298 Chirality : 0.045 0.349 4350 Planarity : 0.004 0.043 4097 Dihedral : 4.469 45.748 3355 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.91 % Rotamer: Outliers : 2.57 % Allowed : 9.32 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3105 helix: 1.80 (0.19), residues: 768 sheet: 0.11 (0.18), residues: 750 loop : -0.42 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 894 TYR 0.017 0.001 TYR B 803 PHE 0.014 0.002 PHE C 622 TRP 0.009 0.001 TRP B 766 HIS 0.004 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (24208) covalent geometry : angle 0.55450 / 0.28 (33190) SS BOND : bond 0.00464 / 0.32 ( 45) SS BOND : angle 2.23900 / 1.56 ( 90) hydrogen bonds : bond 0.06341 / 4.24 ( 963) hydrogen bonds : angle 4.78263 / 3.34 ( 2808) link_ALPHA1-3 : bond 0.00549 / 0.33 ( 6) link_ALPHA1-3 : angle 1.45841 / 0.96 ( 18) link_ALPHA1-6 : bond 0.00524 / 0.32 ( 6) link_ALPHA1-6 : angle 1.43526 / 0.97 ( 18) link_BETA1-4 : bond 0.00379 / 0.26 ( 29) link_BETA1-4 : angle 1.51413 / 1.16 ( 87) link_NAG-ASN : bond 0.00583 / 0.44 ( 66) link_NAG-ASN : angle 2.94330 / 2.05 ( 198) *********************** 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 210 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.863 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 913 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8616 (pp) REVERT: A 1277 THR cc_start: 0.9085 (t) cc_final: 0.8805 (p) REVERT: B 891 MET cc_start: 0.8328 (tpt) cc_final: 0.7772 (tpp) REVERT: B 913 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8550 (pp) REVERT: B 1137 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7620 (mtp85) REVERT: B 1277 THR cc_start: 0.9103 (t) cc_final: 0.8793 (p) REVERT: C 913 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8580 (pp) outliers start: 51 outliers final: 39 residues processed: 200 average time/residue: 0.1340 time to fit residues: 45.1201 Evaluate side-chains 195 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 253 GLN 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 803 TYR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 913 LEU 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 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 913 LEU 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 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 797 CYS Chi-restraints excluded: chain C residue 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1034 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 271 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 276 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 304 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.108547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.097098 restraints weight = 33613.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.095395 restraints weight = 56678.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.093476 restraints weight = 60669.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.092691 restraints weight = 70601.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.093091 restraints weight = 54793.991| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24360 Z= 0.127 Angle : 0.549 18.901 33601 Z= 0.269 Chirality : 0.044 0.338 4350 Planarity : 0.004 0.044 4097 Dihedral : 4.283 45.847 3355 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.23 % Rotamer: Outliers : 2.17 % Allowed : 10.08 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3105 helix: 2.07 (0.20), residues: 747 sheet: 0.13 (0.18), residues: 762 loop : -0.38 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 894 TYR 0.012 0.001 TYR A1016 PHE 0.010 0.001 PHE B 772 TRP 0.007 0.001 TRP A 426 HIS 0.002 0.001 HIS B1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (24208) covalent geometry : angle 0.49120 / 0.25 (33190) SS BOND : bond 0.00337 / 0.23 ( 45) SS BOND : angle 2.00523 / 1.34 ( 90) hydrogen bonds : bond 0.05558 / 3.73 ( 963) hydrogen bonds : angle 4.58534 / 3.20 ( 2808) link_ALPHA1-3 : bond 0.00605 / 0.37 ( 6) link_ALPHA1-3 : angle 1.40556 / 0.92 ( 18) link_ALPHA1-6 : bond 0.00556 / 0.34 ( 6) link_ALPHA1-6 : angle 1.41777 / 0.96 ( 18) link_BETA1-4 : bond 0.00381 / 0.27 ( 29) link_BETA1-4 : angle 1.30753 / 1.00 ( 87) link_NAG-ASN : bond 0.00560 / 0.43 ( 66) link_NAG-ASN : angle 2.79626 / 1.93 ( 198) *********************** 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 206 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 913 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8659 (pp) REVERT: A 1277 THR cc_start: 0.9155 (t) cc_final: 0.8865 (p) REVERT: B 891 MET cc_start: 0.8278 (tpt) cc_final: 0.8050 (tpp) REVERT: B 913 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8565 (pp) REVERT: B 1137 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7633 (mtp85) REVERT: B 1277 THR cc_start: 0.9159 (t) cc_final: 0.8831 (p) REVERT: C 913 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8594 (pp) outliers start: 43 outliers final: 37 residues processed: 196 average time/residue: 0.1306 time to fit residues: 42.4691 Evaluate side-chains 198 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 295 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 803 TYR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 913 LEU 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 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 913 LEU 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 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 797 CYS Chi-restraints excluded: chain C residue 803 TYR Chi-restraints excluded: chain C residue 806 ILE Chi-restraints excluded: chain C residue 880 SER Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1034 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 247 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 225 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.108459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.096404 restraints weight = 33629.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.095640 restraints weight = 51057.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.094518 restraints weight = 55819.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.094029 restraints weight = 52716.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.093632 restraints weight = 46801.344| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24360 Z= 0.153 Angle : 0.566 18.915 33601 Z= 0.276 Chirality : 0.044 0.351 4350 Planarity : 0.004 0.044 4097 Dihedral : 4.328 45.594 3355 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.09 % Favored : 97.81 % Rotamer: Outliers : 2.32 % Allowed : 10.03 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3105 helix: 1.87 (0.19), residues: 768 sheet: 0.12 (0.18), residues: 750 loop : -0.40 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 894 TYR 0.012 0.001 TYR A1016 PHE 0.011 0.001 PHE C 622 TRP 0.007 0.001 TRP B 766 HIS 0.002 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (24208) covalent geometry : angle 0.51056 / 0.26 (33190) SS BOND : bond 0.00393 / 0.27 ( 45) SS BOND : angle 1.95803 / 1.35 ( 90) hydrogen bonds : bond 0.05824 / 3.90 ( 963) hydrogen bonds : angle 4.63436 / 3.24 ( 2808) link_ALPHA1-3 : bond 0.00631 / 0.39 ( 6) link_ALPHA1-3 : angle 1.44275 / 0.95 ( 18) link_ALPHA1-6 : bond 0.00537 / 0.32 ( 6) link_ALPHA1-6 : angle 1.43521 / 0.97 ( 18) link_BETA1-4 : bond 0.00368 / 0.26 ( 29) link_BETA1-4 : angle 1.39617 / 1.06 ( 87) link_NAG-ASN : bond 0.00547 / 0.41 ( 66) link_NAG-ASN : angle 2.77097 / 1.93 ( 198) ********************** 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 205 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.833 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 913 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8653 (pp) REVERT: A 1277 THR cc_start: 0.9154 (t) cc_final: 0.8858 (p) REVERT: B 891 MET cc_start: 0.8288 (tpt) cc_final: 0.8039 (tpp) REVERT: B 913 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8558 (pp) REVERT: B 1137 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7622 (mtp85) REVERT: B 1277 THR cc_start: 0.9166 (t) cc_final: 0.8834 (p) REVERT: C 913 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8596 (pp) outliers start: 46 outliers final: 40 residues processed: 196 average time/residue: 0.1368 time to fit residues: 44.7472 Evaluate side-chains 198 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 295 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 803 TYR Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 913 LEU 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 803 TYR Chi-restraints excluded: chain B residue 806 ILE Chi-restraints excluded: chain B residue 913 LEU 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 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 797 CYS 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 880 SER Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1034 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 238 optimal weight: 0.3980 chunk 200 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.108367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.097256 restraints weight = 33543.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.095889 restraints weight = 53839.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.094567 restraints weight = 57673.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.094119 restraints weight = 57522.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.094287 restraints weight = 47386.986| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24360 Z= 0.137 Angle : 0.549 18.857 33601 Z= 0.269 Chirality : 0.044 0.345 4350 Planarity : 0.004 0.043 4097 Dihedral : 4.271 45.644 3355 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.84 % Favored : 98.07 % Rotamer: Outliers : 2.27 % Allowed : 10.18 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 3105 helix: 2.05 (0.20), residues: 747 sheet: 0.13 (0.18), residues: 762 loop : -0.37 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 894 TYR 0.012 0.001 TYR A1016 PHE 0.012 0.001 PHE B 772 TRP 0.007 0.001 TRP A 426 HIS 0.002 0.001 HIS B1218 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (24208) covalent geometry : angle 0.49418 / 0.26 (33190) SS BOND : bond 0.00355 / 0.24 ( 45) SS BOND : angle 1.96507 / 1.34 ( 90) hydrogen bonds : bond 0.05610 / 3.76 ( 963) hydrogen bonds : angle 4.57465 / 3.19 ( 2808) link_ALPHA1-3 : bond 0.00626 / 0.38 ( 6) link_ALPHA1-3 : angle 1.42175 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00548 / 0.33 ( 6) link_ALPHA1-6 : angle 1.43589 / 0.97 ( 18) link_BETA1-4 : bond 0.00376 / 0.27 ( 29) link_BETA1-4 : angle 1.33310 / 1.01 ( 87) link_NAG-ASN : bond 0.00532 / 0.41 ( 66) link_NAG-ASN : angle 2.69183 / 1.86 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3365.37 seconds wall clock time: 59 minutes 5.16 seconds (3545.16 seconds total)