Starting phenix.real_space_refine on Mon Jun 23 18:50:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybm_33726/06_2025/7ybm_33726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybm_33726/06_2025/7ybm_33726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybm_33726/06_2025/7ybm_33726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybm_33726/06_2025/7ybm_33726.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybm_33726/06_2025/7ybm_33726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybm_33726/06_2025/7ybm_33726.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 114 5.16 5 C 17439 2.51 5 N 4416 2.21 5 O 5487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.65s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27456 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.53, per 1000 atoms: 0.64 Number of scatterers: 27456 At special positions: 0 Unit cell: (142.31, 150.87, 196.88, 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 114 16.00 O 5487 8.00 N 4416 7.00 C 17439 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG G 2 " - " MAN G 3 " " NAG H 2 " - " MAN H 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 343 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 343 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 17 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 8.30 Conformation dependent library (CDL) restraints added in 3.6 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 47 sheets defined 26.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.190A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.755A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.925A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.541A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.909A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.730A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.577A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.860A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.600A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 939 removed outlier: 3.703A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.544A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.720A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.715A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.871A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 389' Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.944A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.754A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.321A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.739A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.584A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.534A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.704A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.806A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.648A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.092A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 988 through 1033 removed outlier: 3.910A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.631A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.608A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.789A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 4.074A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.771A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.805A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.677A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.683A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 939 removed outlier: 3.668A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.917A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.328A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.039A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.319A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 94 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 42 through 43 current: chain 'B' and resid 538 through 543 removed outlier: 3.549A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 546 through 547 current: chain 'B' and resid 573 through 577 removed outlier: 5.333A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 54 removed outlier: 7.559A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 85 current: chain 'A' and resid 116 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.506A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.147A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.887A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.295A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.852A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.798A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 718 through 728 current: chain 'A' and resid 1059 through 1069 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.395A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.551A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 60 through 64 current: chain 'B' and resid 187 through 189 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 187 through 189 current: chain 'B' and resid 200 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 54 removed outlier: 3.504A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.975A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.570A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.529A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.607A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.554A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 718 through 728 current: chain 'B' and resid 1059 through 1069 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.534A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.251A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.543A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.559A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.297A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.937A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.772A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.601A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1076 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.597A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 910 hydrogen bonds defined for protein. 2493 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: 12.73 Time building geometry restraints manager: 9.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8549 1.34 - 1.46: 7183 1.46 - 1.59: 12181 1.59 - 1.71: 2 1.71 - 1.83: 144 Bond restraints: 28059 Sorted by residual: bond pdb=" C PRO C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.12e-02 7.97e+03 1.36e+01 bond pdb=" CB PRO B 589 " pdb=" CG PRO B 589 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.74e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C5 MAN U 3 " pdb=" O5 MAN U 3 " ideal model delta sigma weight residual 1.418 1.464 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" C5 MAN J 3 " pdb=" O5 MAN J 3 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 28054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 37404 2.36 - 4.72: 666 4.72 - 7.09: 68 7.09 - 9.45: 10 9.45 - 11.81: 3 Bond angle restraints: 38151 Sorted by residual: angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.46e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.31 110.41 -7.10 8.90e-01 1.26e+00 6.37e+01 angle pdb=" CA PRO B 589 " pdb=" N PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 112.00 100.92 11.08 1.40e+00 5.10e-01 6.27e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.27 110.23 -6.96 9.00e-01 1.23e+00 5.98e+01 angle pdb=" N PRO B 899 " pdb=" CA PRO B 899 " pdb=" CB PRO B 899 " ideal model delta sigma weight residual 103.51 110.05 -6.54 9.60e-01 1.09e+00 4.65e+01 ... (remaining 38146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 17098 25.06 - 50.11: 832 50.11 - 75.17: 110 75.17 - 100.23: 73 100.23 - 125.29: 37 Dihedral angle restraints: 18150 sinusoidal: 8517 harmonic: 9633 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -171.05 85.05 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -167.39 81.39 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -159.80 73.80 1 1.00e+01 1.00e-02 6.92e+01 ... (remaining 18147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 4624 0.240 - 0.479: 11 0.479 - 0.719: 0 0.719 - 0.959: 1 0.959 - 1.198: 1 Chirality restraints: 4637 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN B 717 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 4634 not shown) Planarity restraints: 4826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 588 " 0.094 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO B 589 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " -0.004 2.00e-02 2.50e+03 3.86e-02 1.87e+01 pdb=" CG ASN B 717 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 588 " 0.069 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 589 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.055 5.00e-02 4.00e+02 ... (remaining 4823 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 416 2.65 - 3.22: 25520 3.22 - 3.78: 40434 3.78 - 4.34: 55053 4.34 - 4.90: 90004 Nonbonded interactions: 211427 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.092 3.040 nonbonded pdb=" OE2 GLU B 988 " pdb=" OG SER C 383 " model vdw 2.159 3.040 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.164 3.040 nonbonded pdb=" O ALA B 924 " pdb=" ND2 ASN B 928 " model vdw 2.170 3.120 nonbonded pdb=" OG SER A 383 " pdb=" OE2 GLU C 988 " model vdw 2.170 3.040 ... (remaining 211422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 67.690 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.004 0.148 28211 Z= 0.227 Angle : 0.851 20.188 38568 Z= 0.437 Chirality : 0.052 1.198 4637 Planarity : 0.005 0.134 4770 Dihedral : 16.149 125.287 11835 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.07 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3267 helix: 1.63 (0.20), residues: 747 sheet: -0.37 (0.22), residues: 555 loop : -1.28 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 633 HIS 0.021 0.001 HIS A 66 PHE 0.024 0.001 PHE C 275 TYR 0.017 0.001 TYR B1138 ARG 0.007 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 56) link_NAG-ASN : angle 5.26762 ( 168) link_ALPHA1-4 : bond 0.00601 ( 21) link_ALPHA1-4 : angle 1.92162 ( 63) link_BETA1-4 : bond 0.00683 ( 33) link_BETA1-4 : angle 1.60079 ( 99) hydrogen bonds : bond 0.19630 ( 910) hydrogen bonds : angle 7.52109 ( 2493) link_BETA1-6 : bond 0.01071 ( 3) link_BETA1-6 : angle 1.12912 ( 9) SS BOND : bond 0.00303 ( 39) SS BOND : angle 1.20240 ( 78) covalent geometry : bond 0.00447 (28059) covalent geometry : angle 0.77034 (38151) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.5873 (t) cc_final: 0.5555 (t) REVERT: C 735 SER cc_start: 0.7570 (t) cc_final: 0.7368 (t) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.4058 time to fit residues: 151.4514 Evaluate side-chains 158 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 138 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 164 ASN A 317 ASN A 394 ASN A 437 ASN A 965 GLN B 66 HIS B 317 ASN B 542 ASN B 644 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.211150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178395 restraints weight = 44288.912| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.71 r_work: 0.3807 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28211 Z= 0.161 Angle : 0.756 18.491 38568 Z= 0.348 Chirality : 0.047 0.533 4637 Planarity : 0.005 0.073 4770 Dihedral : 13.291 107.114 5883 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.88 % Favored : 94.03 % Rotamer: Outliers : 0.62 % Allowed : 5.26 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3267 helix: 1.71 (0.20), residues: 738 sheet: -0.47 (0.21), residues: 609 loop : -1.37 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.006 0.001 HIS C 66 PHE 0.022 0.002 PHE B 643 TYR 0.023 0.002 TYR A 266 ARG 0.006 0.001 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 56) link_NAG-ASN : angle 4.74128 ( 168) link_ALPHA1-4 : bond 0.01166 ( 21) link_ALPHA1-4 : angle 2.57466 ( 63) link_BETA1-4 : bond 0.00562 ( 33) link_BETA1-4 : angle 1.10811 ( 99) hydrogen bonds : bond 0.05922 ( 910) hydrogen bonds : angle 6.06041 ( 2493) link_BETA1-6 : bond 0.01596 ( 3) link_BETA1-6 : angle 1.42764 ( 9) SS BOND : bond 0.00390 ( 39) SS BOND : angle 1.51413 ( 78) covalent geometry : bond 0.00364 (28059) covalent geometry : angle 0.67816 (38151) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.4483 (p-90) cc_final: 0.3878 (p-90) REVERT: A 738 CYS cc_start: 0.7477 (t) cc_final: 0.7106 (t) REVERT: B 509 ARG cc_start: 0.4256 (ttm170) cc_final: 0.4049 (ttp-170) outliers start: 18 outliers final: 13 residues processed: 186 average time/residue: 0.3595 time to fit residues: 111.3261 Evaluate side-chains 161 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 319 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 279 optimal weight: 10.0000 chunk 323 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 965 GLN B 146 HIS B 317 ASN B 542 ASN B 580 GLN C 644 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.209899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.176704 restraints weight = 44459.048| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.69 r_work: 0.3861 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28211 Z= 0.155 Angle : 0.743 17.556 38568 Z= 0.336 Chirality : 0.046 0.514 4637 Planarity : 0.004 0.052 4770 Dihedral : 12.191 101.871 5883 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 1.18 % Allowed : 8.00 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 3267 helix: 1.68 (0.20), residues: 741 sheet: -0.43 (0.21), residues: 636 loop : -1.43 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.005 0.001 HIS C1058 PHE 0.021 0.002 PHE A 318 TYR 0.017 0.001 TYR B1067 ARG 0.005 0.001 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 56) link_NAG-ASN : angle 4.65776 ( 168) link_ALPHA1-4 : bond 0.01439 ( 21) link_ALPHA1-4 : angle 2.79312 ( 63) link_BETA1-4 : bond 0.00434 ( 33) link_BETA1-4 : angle 1.21689 ( 99) hydrogen bonds : bond 0.05705 ( 910) hydrogen bonds : angle 5.79403 ( 2493) link_BETA1-6 : bond 0.01477 ( 3) link_BETA1-6 : angle 2.00800 ( 9) SS BOND : bond 0.00338 ( 39) SS BOND : angle 1.38375 ( 78) covalent geometry : bond 0.00349 (28059) covalent geometry : angle 0.66396 (38151) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.5036 (p0) cc_final: 0.4771 (p0) REVERT: A 738 CYS cc_start: 0.6781 (t) cc_final: 0.6528 (t) REVERT: A 878 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7750 (tt) REVERT: B 509 ARG cc_start: 0.4290 (ttm170) cc_final: 0.3975 (ttp-170) REVERT: C 878 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8288 (tt) outliers start: 34 outliers final: 20 residues processed: 190 average time/residue: 0.3596 time to fit residues: 114.9125 Evaluate side-chains 167 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 76 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 126 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 437 ASN A1011 GLN B 146 HIS B 185 ASN B 644 GLN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 317 ASN C 965 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.203966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.170148 restraints weight = 44715.913| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 2.71 r_work: 0.3776 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 28211 Z= 0.244 Angle : 0.862 16.085 38568 Z= 0.395 Chirality : 0.050 0.515 4637 Planarity : 0.005 0.050 4770 Dihedral : 10.277 86.683 5883 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.22 % Favored : 92.68 % Rotamer: Outliers : 1.90 % Allowed : 10.31 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3267 helix: 1.23 (0.19), residues: 744 sheet: -0.75 (0.20), residues: 648 loop : -1.68 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.011 0.002 HIS C1058 PHE 0.027 0.002 PHE B 906 TYR 0.024 0.002 TYR B1067 ARG 0.007 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 56) link_NAG-ASN : angle 4.72967 ( 168) link_ALPHA1-4 : bond 0.01866 ( 21) link_ALPHA1-4 : angle 3.38736 ( 63) link_BETA1-4 : bond 0.00415 ( 33) link_BETA1-4 : angle 1.42084 ( 99) hydrogen bonds : bond 0.07546 ( 910) hydrogen bonds : angle 6.15382 ( 2493) link_BETA1-6 : bond 0.01910 ( 3) link_BETA1-6 : angle 2.38599 ( 9) SS BOND : bond 0.00704 ( 39) SS BOND : angle 1.86706 ( 78) covalent geometry : bond 0.00580 (28059) covalent geometry : angle 0.78724 (38151) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 3.052 Fit side-chains revert: symmetry clash REVERT: A 738 CYS cc_start: 0.6894 (t) cc_final: 0.6671 (t) REVERT: A 878 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8032 (tt) REVERT: A 957 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8310 (tm-30) REVERT: B 362 VAL cc_start: 0.7266 (t) cc_final: 0.7033 (t) REVERT: B 364 ASP cc_start: 0.5421 (OUTLIER) cc_final: 0.5051 (p0) REVERT: B 509 ARG cc_start: 0.4564 (ttm170) cc_final: 0.4148 (ttp-170) REVERT: C 403 ARG cc_start: 0.6255 (mtm180) cc_final: 0.5917 (tpp80) REVERT: C 850 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7725 (mp) REVERT: C 878 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8443 (tt) outliers start: 55 outliers final: 33 residues processed: 200 average time/residue: 0.3534 time to fit residues: 120.3745 Evaluate side-chains 167 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 5 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 231 optimal weight: 20.0000 chunk 129 optimal weight: 0.0870 chunk 52 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 232 optimal weight: 30.0000 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 146 HIS B 644 GLN C 542 ASN C1002 GLN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.207067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173421 restraints weight = 44358.480| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.75 r_work: 0.3799 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28211 Z= 0.136 Angle : 0.736 15.867 38568 Z= 0.326 Chirality : 0.045 0.505 4637 Planarity : 0.004 0.052 4770 Dihedral : 8.896 87.867 5883 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 1.66 % Allowed : 11.70 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3267 helix: 1.73 (0.20), residues: 726 sheet: -0.57 (0.20), residues: 669 loop : -1.55 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS A 519 PHE 0.013 0.001 PHE B 192 TYR 0.019 0.001 TYR A 265 ARG 0.006 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 56) link_NAG-ASN : angle 4.24147 ( 168) link_ALPHA1-4 : bond 0.01941 ( 21) link_ALPHA1-4 : angle 3.28871 ( 63) link_BETA1-4 : bond 0.00529 ( 33) link_BETA1-4 : angle 1.27164 ( 99) hydrogen bonds : bond 0.05518 ( 910) hydrogen bonds : angle 5.65247 ( 2493) link_BETA1-6 : bond 0.02120 ( 3) link_BETA1-6 : angle 2.40504 ( 9) SS BOND : bond 0.00333 ( 39) SS BOND : angle 1.51326 ( 78) covalent geometry : bond 0.00281 (28059) covalent geometry : angle 0.66310 (38151) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 2.773 Fit side-chains revert: symmetry clash REVERT: A 738 CYS cc_start: 0.6751 (t) cc_final: 0.6469 (t) REVERT: A 878 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7659 (tt) REVERT: A 954 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8249 (mm-40) REVERT: B 364 ASP cc_start: 0.5465 (OUTLIER) cc_final: 0.5264 (p0) REVERT: C 321 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8009 (mp10) REVERT: C 878 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8395 (tt) outliers start: 48 outliers final: 24 residues processed: 193 average time/residue: 0.3300 time to fit residues: 109.0469 Evaluate side-chains 162 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 328 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 74 optimal weight: 0.0670 chunk 158 optimal weight: 10.0000 chunk 172 optimal weight: 0.0570 chunk 34 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 437 ASN B 146 HIS B 542 ASN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.204598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.164824 restraints weight = 44441.021| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.03 r_work: 0.3490 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28211 Z= 0.191 Angle : 0.778 14.928 38568 Z= 0.350 Chirality : 0.047 0.506 4637 Planarity : 0.004 0.045 4770 Dihedral : 8.342 85.500 5883 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.90 % Rotamer: Outliers : 2.15 % Allowed : 12.53 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3267 helix: 1.66 (0.20), residues: 726 sheet: -0.60 (0.21), residues: 609 loop : -1.63 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.007 0.001 HIS C1058 PHE 0.018 0.002 PHE C 192 TYR 0.019 0.002 TYR B1067 ARG 0.005 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 56) link_NAG-ASN : angle 4.34045 ( 168) link_ALPHA1-4 : bond 0.01907 ( 21) link_ALPHA1-4 : angle 3.37644 ( 63) link_BETA1-4 : bond 0.00385 ( 33) link_BETA1-4 : angle 1.37630 ( 99) hydrogen bonds : bond 0.06351 ( 910) hydrogen bonds : angle 5.75818 ( 2493) link_BETA1-6 : bond 0.01876 ( 3) link_BETA1-6 : angle 2.35879 ( 9) SS BOND : bond 0.00418 ( 39) SS BOND : angle 1.61608 ( 78) covalent geometry : bond 0.00444 (28059) covalent geometry : angle 0.70581 (38151) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 2.798 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7797 (mp0) REVERT: A 560 LEU cc_start: 0.5330 (OUTLIER) cc_final: 0.5121 (tp) REVERT: A 738 CYS cc_start: 0.7005 (t) cc_final: 0.6753 (t) REVERT: A 878 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7953 (tt) REVERT: B 1144 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: C 86 PHE cc_start: 0.1907 (t80) cc_final: 0.1681 (t80) REVERT: C 321 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: C 403 ARG cc_start: 0.7009 (mtm180) cc_final: 0.6253 (tpp80) REVERT: C 878 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8391 (tt) outliers start: 62 outliers final: 41 residues processed: 197 average time/residue: 0.3284 time to fit residues: 110.1843 Evaluate side-chains 177 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1144 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 15 optimal weight: 7.9990 chunk 306 optimal weight: 1.9990 chunk 281 optimal weight: 8.9990 chunk 264 optimal weight: 0.0770 chunk 154 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 125 optimal weight: 0.2980 chunk 170 optimal weight: 10.0000 chunk 291 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 99 ASN B 146 HIS B 542 ASN C 542 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.204982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.170118 restraints weight = 44231.207| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.79 r_work: 0.3784 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28211 Z= 0.135 Angle : 0.720 14.559 38568 Z= 0.320 Chirality : 0.045 0.503 4637 Planarity : 0.004 0.044 4770 Dihedral : 7.667 85.899 5883 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 2.01 % Allowed : 12.88 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3267 helix: 1.71 (0.20), residues: 750 sheet: -0.57 (0.21), residues: 609 loop : -1.51 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.005 0.001 HIS A 519 PHE 0.013 0.001 PHE B 192 TYR 0.017 0.001 TYR A 265 ARG 0.010 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 56) link_NAG-ASN : angle 4.08962 ( 168) link_ALPHA1-4 : bond 0.01920 ( 21) link_ALPHA1-4 : angle 3.27305 ( 63) link_BETA1-4 : bond 0.00460 ( 33) link_BETA1-4 : angle 1.30694 ( 99) hydrogen bonds : bond 0.05364 ( 910) hydrogen bonds : angle 5.51241 ( 2493) link_BETA1-6 : bond 0.01916 ( 3) link_BETA1-6 : angle 2.22861 ( 9) SS BOND : bond 0.00318 ( 39) SS BOND : angle 1.59512 ( 78) covalent geometry : bond 0.00286 (28059) covalent geometry : angle 0.64997 (38151) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 3.056 Fit side-chains revert: symmetry clash REVERT: A 738 CYS cc_start: 0.6811 (t) cc_final: 0.6556 (t) REVERT: A 878 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7702 (tt) REVERT: A 954 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8252 (mm-40) REVERT: A 977 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8534 (mp) REVERT: C 48 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8421 (mp) REVERT: C 321 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: C 850 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7737 (mp) REVERT: C 878 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8352 (tt) outliers start: 58 outliers final: 36 residues processed: 198 average time/residue: 0.3414 time to fit residues: 118.2187 Evaluate side-chains 179 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 74 optimal weight: 0.0060 chunk 136 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 314 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 291 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS B 542 ASN C 542 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.206580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.173525 restraints weight = 44580.860| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.70 r_work: 0.3835 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28211 Z= 0.125 Angle : 0.701 14.660 38568 Z= 0.313 Chirality : 0.044 0.501 4637 Planarity : 0.004 0.045 4770 Dihedral : 7.247 85.582 5883 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 1.80 % Allowed : 13.08 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3267 helix: 1.81 (0.20), residues: 750 sheet: -0.54 (0.20), residues: 639 loop : -1.43 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.004 0.001 HIS A 519 PHE 0.029 0.001 PHE C 92 TYR 0.020 0.001 TYR C 170 ARG 0.009 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 56) link_NAG-ASN : angle 3.98152 ( 168) link_ALPHA1-4 : bond 0.01866 ( 21) link_ALPHA1-4 : angle 3.28299 ( 63) link_BETA1-4 : bond 0.00455 ( 33) link_BETA1-4 : angle 1.28956 ( 99) hydrogen bonds : bond 0.04976 ( 910) hydrogen bonds : angle 5.37768 ( 2493) link_BETA1-6 : bond 0.01869 ( 3) link_BETA1-6 : angle 2.12665 ( 9) SS BOND : bond 0.00287 ( 39) SS BOND : angle 1.30220 ( 78) covalent geometry : bond 0.00254 (28059) covalent geometry : angle 0.63320 (38151) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 3.084 Fit side-chains revert: symmetry clash REVERT: A 738 CYS cc_start: 0.6685 (t) cc_final: 0.6443 (t) REVERT: A 878 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7640 (tt) REVERT: C 48 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8363 (mp) REVERT: C 321 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: C 878 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8342 (tt) outliers start: 52 outliers final: 40 residues processed: 192 average time/residue: 0.3288 time to fit residues: 109.2005 Evaluate side-chains 180 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 171 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 312 optimal weight: 0.7980 chunk 328 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 242 optimal weight: 30.0000 chunk 291 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 146 HIS C 542 ASN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.206681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.172977 restraints weight = 44704.011| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.74 r_work: 0.3824 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28211 Z= 0.123 Angle : 0.695 14.852 38568 Z= 0.310 Chirality : 0.044 0.500 4637 Planarity : 0.004 0.046 4770 Dihedral : 6.974 84.180 5883 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 1.80 % Allowed : 13.43 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3267 helix: 1.86 (0.20), residues: 750 sheet: -0.46 (0.20), residues: 636 loop : -1.41 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.004 0.001 HIS A 519 PHE 0.028 0.001 PHE C 92 TYR 0.016 0.001 TYR A 265 ARG 0.011 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 56) link_NAG-ASN : angle 3.90262 ( 168) link_ALPHA1-4 : bond 0.01823 ( 21) link_ALPHA1-4 : angle 3.26012 ( 63) link_BETA1-4 : bond 0.00449 ( 33) link_BETA1-4 : angle 1.27710 ( 99) hydrogen bonds : bond 0.04828 ( 910) hydrogen bonds : angle 5.27950 ( 2493) link_BETA1-6 : bond 0.01824 ( 3) link_BETA1-6 : angle 2.07447 ( 9) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.14426 ( 78) covalent geometry : bond 0.00255 (28059) covalent geometry : angle 0.62872 (38151) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.6690 (t) cc_final: 0.6443 (t) REVERT: A 878 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7699 (tt) REVERT: B 560 LEU cc_start: 0.5158 (OUTLIER) cc_final: 0.4933 (tp) REVERT: C 48 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8258 (mp) REVERT: C 321 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: C 878 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8327 (tt) outliers start: 52 outliers final: 41 residues processed: 192 average time/residue: 0.3251 time to fit residues: 107.1376 Evaluate side-chains 181 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 6 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 146 HIS B 542 ASN C 542 ASN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.205323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.171141 restraints weight = 44449.237| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.80 r_work: 0.3801 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28211 Z= 0.144 Angle : 0.709 14.599 38568 Z= 0.320 Chirality : 0.045 0.499 4637 Planarity : 0.004 0.049 4770 Dihedral : 6.858 80.436 5883 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 1.70 % Allowed : 13.60 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3267 helix: 1.96 (0.20), residues: 729 sheet: -0.50 (0.20), residues: 636 loop : -1.46 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 353 HIS 0.005 0.001 HIS A 519 PHE 0.021 0.001 PHE C 543 TYR 0.021 0.001 TYR C 170 ARG 0.017 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 56) link_NAG-ASN : angle 3.90483 ( 168) link_ALPHA1-4 : bond 0.01802 ( 21) link_ALPHA1-4 : angle 3.23950 ( 63) link_BETA1-4 : bond 0.00417 ( 33) link_BETA1-4 : angle 1.29220 ( 99) hydrogen bonds : bond 0.05203 ( 910) hydrogen bonds : angle 5.32615 ( 2493) link_BETA1-6 : bond 0.01766 ( 3) link_BETA1-6 : angle 2.08393 ( 9) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.27355 ( 78) covalent geometry : bond 0.00323 (28059) covalent geometry : angle 0.64407 (38151) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.7230 (t) cc_final: 0.6997 (t) REVERT: A 878 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7716 (tt) REVERT: C 48 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8403 (mp) REVERT: C 321 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: C 850 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7798 (mp) REVERT: C 878 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8356 (tt) outliers start: 49 outliers final: 41 residues processed: 185 average time/residue: 0.4123 time to fit residues: 132.4750 Evaluate side-chains 182 residues out of total 2898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 214 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 288 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 286 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.205377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.171472 restraints weight = 44583.724| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.71 r_work: 0.3809 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 28211 Z= 0.166 Angle : 0.819 59.194 38568 Z= 0.414 Chirality : 0.046 0.709 4637 Planarity : 0.005 0.146 4770 Dihedral : 6.869 80.431 5883 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 1.63 % Allowed : 13.78 % Favored : 84.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3267 helix: 1.94 (0.20), residues: 732 sheet: -0.49 (0.20), residues: 636 loop : -1.46 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 353 HIS 0.004 0.001 HIS A 519 PHE 0.019 0.001 PHE C 543 TYR 0.017 0.001 TYR A 265 ARG 0.012 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 56) link_NAG-ASN : angle 3.90331 ( 168) link_ALPHA1-4 : bond 0.01793 ( 21) link_ALPHA1-4 : angle 3.24470 ( 63) link_BETA1-4 : bond 0.00441 ( 33) link_BETA1-4 : angle 1.29220 ( 99) hydrogen bonds : bond 0.05156 ( 910) hydrogen bonds : angle 5.32318 ( 2493) link_BETA1-6 : bond 0.01730 ( 3) link_BETA1-6 : angle 2.08560 ( 9) SS BOND : bond 0.00423 ( 39) SS BOND : angle 1.24272 ( 78) covalent geometry : bond 0.00354 (28059) covalent geometry : angle 0.76511 (38151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11727.39 seconds wall clock time: 204 minutes 33.59 seconds (12273.59 seconds total)