Starting phenix.real_space_refine on Mon Jun 23 11:59:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dez_46804/06_2025/9dez_46804.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dez_46804/06_2025/9dez_46804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dez_46804/06_2025/9dez_46804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dez_46804/06_2025/9dez_46804.map" model { file = "/net/cci-nas-00/data/ceres_data/9dez_46804/06_2025/9dez_46804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dez_46804/06_2025/9dez_46804.cif" } resolution = 2.6 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= 0.005 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 141 5.16 5 C 17169 2.51 5 N 4503 2.21 5 O 5322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 1.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27135 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 7095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7095 Classifications: {'peptide': 956} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 922} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 10, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 7095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7095 Classifications: {'peptide': 956} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 922} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 10, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 122 Chain: "C" Number of atoms: 7095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7095 Classifications: {'peptide': 956} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 922} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 10, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 122 Chain: "H" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 747 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "I" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 747 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "J" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 747 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "L" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 638 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "M" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 638 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "N" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 638 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 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: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'NAG': 10, 'PAM': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'NAG': 10, 'PAM': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'NAG': 10, 'PAM': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.04, per 1000 atoms: 0.63 Number of scatterers: 27135 At special positions: 0 Unit cell: (126.92, 131.93, 188.71, 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 141 16.00 O 5322 8.00 N 4503 7.00 C 17169 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 710 " distance=2.04 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 912 " distance=2.01 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 710 " distance=2.04 Simple disulfide: pdb=" SG CYS B 901 " - pdb=" SG CYS B 912 " distance=2.01 Simple disulfide: pdb=" SG CYS B 951 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 361 " - pdb=" SG CYS C 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 545 " distance=2.03 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 710 " distance=2.04 Simple disulfide: pdb=" SG CYS C 901 " - pdb=" SG CYS C 912 " distance=2.01 Simple disulfide: pdb=" SG CYS C 951 " - pdb=" SG CYS C 997 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A1201 " - " ASN A1003 " " NAG A1202 " - " ASN A 652 " " NAG A1203 " - " ASN A 494 " " NAG A1204 " - " ASN A 531 " " NAG A1205 " - " ASN A 970 " " NAG A1206 " - " ASN A 99 " " NAG A1207 " - " ASN A 162 " " NAG A1208 " - " ASN A 169 " " NAG A1209 " - " ASN A 505 " " NAG A1210 " - " ASN A 331 " " NAG B1201 " - " ASN B1003 " " NAG B1202 " - " ASN B 652 " " NAG B1203 " - " ASN B 494 " " NAG B1204 " - " ASN B 531 " " NAG B1205 " - " ASN B 970 " " NAG B1206 " - " ASN B 99 " " NAG B1207 " - " ASN B 162 " " NAG B1208 " - " ASN B 169 " " NAG B1209 " - " ASN B 505 " " NAG B1210 " - " ASN B 331 " " NAG C4002 " - " ASN C 162 " " NAG C4003 " - " ASN C 169 " " NAG C4004 " - " ASN C 99 " " NAG C4005 " - " ASN C 331 " " NAG C4006 " - " ASN C 505 " " NAG C4007 " - " ASN C 652 " " NAG C4008 " - " ASN C 531 " " NAG C4009 " - " ASN C 494 " " NAG C4010 " - " ASN C1003 " " NAG C4011 " - " ASN C 970 " " NAG D 1 " - " ASN A 788 " " NAG E 1 " - " ASN A 914 " " NAG F 1 " - " ASN A 661 " " NAG G 1 " - " ASN A 945 " " NAG K 1 " - " ASN A 74 " " NAG O 1 " - " ASN A 241 " " NAG P 1 " - " ASN A 251 " " NAG Q 1 " - " ASN A 311 " " NAG R 1 " - " ASN A 184 " " NAG S 1 " - " ASN A 472 " " NAG T 1 " - " ASN A 526 " " NAG U 1 " - " ASN B 788 " " NAG V 1 " - " ASN B 914 " " NAG W 1 " - " ASN B 661 " " NAG X 1 " - " ASN B 945 " " NAG Y 1 " - " ASN B 74 " " NAG Z 1 " - " ASN B 241 " " NAG a 1 " - " ASN B 251 " " NAG b 1 " - " ASN B 311 " " NAG c 1 " - " ASN B 184 " " NAG d 1 " - " ASN B 472 " " NAG e 1 " - " ASN B 526 " " NAG f 1 " - " ASN C 472 " " NAG g 1 " - " ASN C 241 " " NAG h 1 " - " ASN C 251 " " NAG i 1 " - " ASN C 74 " " NAG j 1 " - " ASN C 311 " " NAG k 1 " - " ASN C 526 " " NAG l 1 " - " ASN C 184 " " NAG m 1 " - " ASN C 661 " " NAG n 1 " - " ASN C 788 " " NAG o 1 " - " ASN C 914 " " NAG p 1 " - " ASN C 945 " Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 3.4 seconds 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6636 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 57 sheets defined 24.6% alpha, 39.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 506 through 510 removed outlier: 3.966A pdb=" N ASN A 509 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 617 through 641 removed outlier: 3.556A pdb=" N ASN A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.966A pdb=" N LYS A 657 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 695 through 701 removed outlier: 4.017A pdb=" N SER A 700 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 707 through 715 removed outlier: 3.572A pdb=" N ASN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 removed outlier: 3.592A pdb=" N THR A 737 " --> pdb=" O THR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 766 removed outlier: 3.602A pdb=" N ALA A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 796 Processing helix chain 'A' and resid 804 through 824 Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'A' and resid 854 through 902 removed outlier: 3.552A pdb=" N GLN A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 889 " --> pdb=" O SER A 885 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1008 through 1013 removed outlier: 3.709A pdb=" N ILE A1012 " --> pdb=" O ASN A1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.967A pdb=" N ASN B 509 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 617 through 641 removed outlier: 3.556A pdb=" N ASN B 621 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.966A pdb=" N LYS B 657 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 683 Processing helix chain 'B' and resid 695 through 701 removed outlier: 4.017A pdb=" N SER B 700 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 706 Processing helix chain 'B' and resid 707 through 715 removed outlier: 3.573A pdb=" N ASN B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 739 removed outlier: 3.591A pdb=" N THR B 737 " --> pdb=" O THR B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 766 removed outlier: 3.603A pdb=" N ALA B 756 " --> pdb=" O PRO B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 796 Processing helix chain 'B' and resid 804 through 824 Processing helix chain 'B' and resid 825 through 834 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 854 through 902 removed outlier: 3.552A pdb=" N GLN B 860 " --> pdb=" O VAL B 856 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 889 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 890 " --> pdb=" O GLN B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1008 through 1013 removed outlier: 3.709A pdb=" N ILE B1012 " --> pdb=" O ASN B1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.966A pdb=" N ASN C 509 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 603 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 617 through 641 removed outlier: 3.555A pdb=" N ASN C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 652 through 657 removed outlier: 3.966A pdb=" N LYS C 657 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 695 through 701 removed outlier: 4.017A pdb=" N SER C 700 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 706 Processing helix chain 'C' and resid 707 through 715 removed outlier: 3.573A pdb=" N ASN C 715 " --> pdb=" O SER C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 739 removed outlier: 3.591A pdb=" N THR C 737 " --> pdb=" O THR C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 766 removed outlier: 3.602A pdb=" N ALA C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 796 Processing helix chain 'C' and resid 804 through 824 Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 845 through 853 Processing helix chain 'C' and resid 854 through 902 removed outlier: 3.552A pdb=" N GLN C 860 " --> pdb=" O VAL C 856 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 864 " --> pdb=" O GLN C 860 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN C 889 " --> pdb=" O SER C 885 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 890 " --> pdb=" O GLN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 1008 through 1013 removed outlier: 3.709A pdb=" N ILE C1012 " --> pdb=" O ASN C1008 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.550A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 85 removed outlier: 3.550A pdb=" N GLU M 85 " --> pdb=" O ALA M 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.551A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 6.419A pdb=" N ASN A 241 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A 91 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 239 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.595A pdb=" N GLN A 256 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 250 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 6.838A pdb=" N CYS A 181 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.799A pdb=" N GLY A 499 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 493 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 297 removed outlier: 3.757A pdb=" N GLN A 293 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 478 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE A 460 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.728A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN A 346 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 310 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET A 348 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 312 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU A 343 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 333 through 335 removed outlier: 4.162A pdb=" N MET A 372 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLN A 376 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N GLN A 412 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N CYS A 378 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N GLU A 410 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N SER A 380 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N ALA A 408 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 587 removed outlier: 6.197A pdb=" N GLU A 570 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 945 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU A 572 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG A 943 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 941 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 576 " --> pdb=" O ASN A 939 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 936 " --> pdb=" O HIS A 917 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS A 917 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 569 through 587 removed outlier: 6.197A pdb=" N GLU A 570 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 945 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU A 572 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG A 943 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE A 941 " --> pdb=" O PRO A 574 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA A 576 " --> pdb=" O ASN A 939 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASN A 945 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN A 968 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 966 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB4, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.013A pdb=" N THR A 643 " --> pdb=" O GLN B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 994 removed outlier: 3.821A pdb=" N GLY A 957 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 81 through 91 removed outlier: 6.419A pdb=" N ASN B 241 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 91 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 239 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.594A pdb=" N GLN B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 250 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 101 through 105 removed outlier: 6.838A pdb=" N CYS B 181 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.799A pdb=" N GLY B 499 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 493 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 293 through 297 removed outlier: 3.758A pdb=" N GLN B 293 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 478 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE B 460 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.728A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU B 306 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU B 344 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 308 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN B 346 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 310 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET B 348 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 312 " --> pdb=" O MET B 348 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU B 343 " --> pdb=" O THR B 417 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 333 through 335 removed outlier: 4.163A pdb=" N MET B 372 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLN B 376 " --> pdb=" O GLN B 412 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLN B 412 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N CYS B 378 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N GLU B 410 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N SER B 380 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N ALA B 408 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AC5, first strand: chain 'B' and resid 569 through 587 removed outlier: 6.195A pdb=" N GLU B 570 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 945 " --> pdb=" O GLU B 570 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 572 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG B 943 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 941 " --> pdb=" O PRO B 574 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 576 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 936 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS B 917 " --> pdb=" O LEU B 936 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 569 through 587 removed outlier: 6.195A pdb=" N GLU B 570 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 945 " --> pdb=" O GLU B 570 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 572 " --> pdb=" O ARG B 943 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG B 943 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 941 " --> pdb=" O PRO B 574 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 576 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASN B 945 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN B 968 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 966 " --> pdb=" O SER B 947 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 593 through 595 Processing sheet with id=AC8, first strand: chain 'B' and resid 643 through 644 removed outlier: 6.019A pdb=" N THR B 643 " --> pdb=" O GLN C 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 991 through 994 removed outlier: 3.821A pdb=" N GLY B 957 " --> pdb=" O LEU B 994 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 81 through 91 removed outlier: 6.419A pdb=" N ASN C 241 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU C 91 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU C 239 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.594A pdb=" N GLN C 256 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 250 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ILE C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.839A pdb=" N CYS C 181 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 280 through 283 removed outlier: 3.798A pdb=" N GLY C 499 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 493 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 293 through 297 removed outlier: 3.757A pdb=" N GLN C 293 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR C 478 " --> pdb=" O SER C 450 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE C 460 " --> pdb=" O TYR C 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.727A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU C 306 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU C 344 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 308 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN C 346 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 310 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N MET C 348 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE C 312 " --> pdb=" O MET C 348 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 343 " --> pdb=" O THR C 417 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 333 through 335 removed outlier: 4.162A pdb=" N MET C 372 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLN C 376 " --> pdb=" O GLN C 412 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N GLN C 412 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N CYS C 378 " --> pdb=" O GLU C 410 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N GLU C 410 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N SER C 380 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N ALA C 408 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 537 through 539 Processing sheet with id=AD9, first strand: chain 'C' and resid 569 through 587 removed outlier: 6.196A pdb=" N GLU C 570 " --> pdb=" O ASN C 945 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 945 " --> pdb=" O GLU C 570 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU C 572 " --> pdb=" O ARG C 943 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG C 943 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE C 941 " --> pdb=" O PRO C 574 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 576 " --> pdb=" O ASN C 939 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 936 " --> pdb=" O HIS C 917 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS C 917 " --> pdb=" O LEU C 936 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 569 through 587 removed outlier: 6.196A pdb=" N GLU C 570 " --> pdb=" O ASN C 945 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN C 945 " --> pdb=" O GLU C 570 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU C 572 " --> pdb=" O ARG C 943 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG C 943 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE C 941 " --> pdb=" O PRO C 574 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 576 " --> pdb=" O ASN C 939 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASN C 945 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN C 968 " --> pdb=" O ASN C 945 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU C 966 " --> pdb=" O SER C 947 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 593 through 595 Processing sheet with id=AE3, first strand: chain 'C' and resid 991 through 994 removed outlier: 3.821A pdb=" N GLY C 957 " --> pdb=" O LEU C 994 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.620A pdb=" N TRP H 36 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS H 42 " --> pdb=" O GLY H 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 46 " --> pdb=" O HIS H 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.465A pdb=" N CYS H 97 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP H 108 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG H 99 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.620A pdb=" N TRP I 36 " --> pdb=" O TYR I 52 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR I 52 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TRP I 38 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS I 42 " --> pdb=" O GLY I 46 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY I 46 " --> pdb=" O HIS I 42 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.465A pdb=" N CYS I 97 " --> pdb=" O TRP I 108 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP I 108 " --> pdb=" O CYS I 97 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG I 99 " --> pdb=" O ASP I 106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.621A pdb=" N TRP J 36 " --> pdb=" O TYR J 52 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR J 52 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TRP J 38 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS J 42 " --> pdb=" O GLY J 46 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.464A pdb=" N CYS J 97 " --> pdb=" O TRP J 108 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP J 108 " --> pdb=" O CYS J 97 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG J 99 " --> pdb=" O ASP J 106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.546A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.711A pdb=" N CYS L 91 " --> pdb=" O PHE L 102 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE L 102 " --> pdb=" O CYS L 91 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR L 93 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL L 100 " --> pdb=" O TYR L 93 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AF7, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.546A pdb=" N TRP M 37 " --> pdb=" O MET M 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.710A pdb=" N CYS M 91 " --> pdb=" O PHE M 102 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE M 102 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR M 93 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL M 100 " --> pdb=" O TYR M 93 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG1, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.546A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.711A pdb=" N CYS N 91 " --> pdb=" O PHE N 102 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE N 102 " --> pdb=" O CYS N 91 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR N 93 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL N 100 " --> pdb=" O TYR N 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 17 through 23 1255 hydrogen bonds defined for protein. 3279 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: 12.88 Time building geometry restraints manager: 9.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8313 1.34 - 1.46: 6228 1.46 - 1.58: 12912 1.58 - 1.70: 0 1.70 - 1.83: 189 Bond restraints: 27642 Sorted by residual: bond pdb=" CG1 ILE C 190 " pdb=" CD1 ILE C 190 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CG1 ILE A 190 " pdb=" CD1 ILE A 190 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.70e+00 bond pdb=" CG1 ILE B 190 " pdb=" CD1 ILE B 190 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.70e+00 bond pdb=" N VAL J 24 " pdb=" CA VAL J 24 " ideal model delta sigma weight residual 1.459 1.477 -0.018 1.25e-02 6.40e+03 2.11e+00 bond pdb=" N VAL H 24 " pdb=" CA VAL H 24 " ideal model delta sigma weight residual 1.459 1.477 -0.018 1.25e-02 6.40e+03 2.11e+00 ... (remaining 27637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 35146 1.57 - 3.14: 2281 3.14 - 4.70: 312 4.70 - 6.27: 43 6.27 - 7.84: 15 Bond angle restraints: 37797 Sorted by residual: angle pdb=" CA TYR L 51 " pdb=" CB TYR L 51 " pdb=" CG TYR L 51 " ideal model delta sigma weight residual 113.90 121.74 -7.84 1.80e+00 3.09e-01 1.90e+01 angle pdb=" CA TYR N 51 " pdb=" CB TYR N 51 " pdb=" CG TYR N 51 " ideal model delta sigma weight residual 113.90 121.73 -7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" CA TYR M 51 " pdb=" CB TYR M 51 " pdb=" CG TYR M 51 " ideal model delta sigma weight residual 113.90 121.70 -7.80 1.80e+00 3.09e-01 1.88e+01 angle pdb=" C PRO A 977 " pdb=" N ARG A 978 " pdb=" CA ARG A 978 " ideal model delta sigma weight residual 122.38 116.47 5.91 1.81e+00 3.05e-01 1.07e+01 angle pdb=" C PRO B 977 " pdb=" N ARG B 978 " pdb=" CA ARG B 978 " ideal model delta sigma weight residual 122.38 116.48 5.90 1.81e+00 3.05e-01 1.06e+01 ... (remaining 37792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.55: 16833 19.55 - 39.10: 672 39.10 - 58.65: 155 58.65 - 78.20: 169 78.20 - 97.75: 114 Dihedral angle restraints: 17943 sinusoidal: 7605 harmonic: 10338 Sorted by residual: dihedral pdb=" CB CYS B 532 " pdb=" SG CYS B 532 " pdb=" SG CYS B 545 " pdb=" CB CYS B 545 " ideal model delta sinusoidal sigma weight residual -86.00 -139.66 53.66 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS C 532 " pdb=" SG CYS C 532 " pdb=" SG CYS C 545 " pdb=" CB CYS C 545 " ideal model delta sinusoidal sigma weight residual -86.00 -139.64 53.64 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS A 532 " pdb=" SG CYS A 532 " pdb=" SG CYS A 545 " pdb=" CB CYS A 545 " ideal model delta sinusoidal sigma weight residual -86.00 -139.63 53.63 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 17940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4083 0.074 - 0.148: 663 0.148 - 0.222: 42 0.222 - 0.295: 9 0.295 - 0.369: 6 Chirality restraints: 4803 Sorted by residual: chirality pdb=" C1 NAG A1204 " pdb=" ND2 ASN A 531 " pdb=" C2 NAG A1204 " pdb=" O5 NAG A1204 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG C4008 " pdb=" ND2 ASN C 531 " pdb=" C2 NAG C4008 " pdb=" O5 NAG C4008 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 531 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.33e+00 ... (remaining 4800 not shown) Planarity restraints: 4812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 505 " -0.025 2.00e-02 2.50e+03 2.61e-02 8.49e+00 pdb=" CG ASN A 505 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 505 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 505 " 0.040 2.00e-02 2.50e+03 pdb=" C1 NAG A1209 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 505 " -0.025 2.00e-02 2.50e+03 2.60e-02 8.46e+00 pdb=" CG ASN C 505 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 505 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 505 " 0.040 2.00e-02 2.50e+03 pdb=" C1 NAG C4006 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 505 " -0.025 2.00e-02 2.50e+03 2.58e-02 8.32e+00 pdb=" CG ASN B 505 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 505 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 505 " 0.040 2.00e-02 2.50e+03 pdb=" C1 NAG B1209 " -0.031 2.00e-02 2.50e+03 ... (remaining 4809 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 11182 2.91 - 3.41: 23051 3.41 - 3.91: 43069 3.91 - 4.40: 48368 4.40 - 4.90: 85185 Nonbonded interactions: 210855 Sorted by model distance: nonbonded pdb=" OG1 THR C 73 " pdb=" O SER C 75 " model vdw 2.414 3.040 nonbonded pdb=" OG1 THR A 73 " pdb=" O SER A 75 " model vdw 2.414 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" O SER B 75 " model vdw 2.414 3.040 nonbonded pdb=" OE2 GLU C 306 " pdb=" OH TYR C 334 " model vdw 2.462 3.040 nonbonded pdb=" OE2 GLU A 306 " pdb=" OH TYR A 334 " model vdw 2.463 3.040 ... (remaining 210850 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 52 through 1017 or resid 1202 through 1210)) selection = (chain 'B' and (resid 52 through 1017 or resid 1202 through 1210)) selection = (chain 'C' and (resid 52 through 1017 or resid 4002 through 4010)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'X' selection = chain 'c' selection = chain 'l' selection = chain 'p' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.920 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: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 66.920 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.240 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.006 0.085 27810 Z= 0.291 Angle : 0.941 10.801 38256 Z= 0.496 Chirality : 0.055 0.369 4803 Planarity : 0.007 0.108 4749 Dihedral : 16.497 97.746 11172 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.65 % Favored : 97.18 % Rotamer: Outliers : 1.03 % Allowed : 2.62 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: -0.38 (0.13), residues: 3513 helix: 0.05 (0.18), residues: 720 sheet: 0.27 (0.17), residues: 849 loop : -0.55 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 108 HIS 0.006 0.002 HIS A 933 PHE 0.031 0.004 PHE B 930 TYR 0.039 0.003 TYR M 51 ARG 0.005 0.001 ARG C 272 Details of bonding type rmsd link_NAG-ASN : bond 0.00915 ( 63) link_NAG-ASN : angle 3.80220 ( 189) link_BETA1-4 : bond 0.01629 ( 60) link_BETA1-4 : angle 3.80912 ( 180) hydrogen bonds : bond 0.14750 ( 1177) hydrogen bonds : angle 7.30612 ( 3279) SS BOND : bond 0.00643 ( 45) SS BOND : angle 1.28176 ( 90) covalent geometry : bond 0.00643 (27642) covalent geometry : angle 0.86648 (37797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 HIS cc_start: 0.8810 (m-70) cc_final: 0.8377 (m-70) REVERT: A 320 GLU cc_start: 0.8634 (tt0) cc_final: 0.8231 (tt0) REVERT: A 322 ARG cc_start: 0.8705 (mtt180) cc_final: 0.8283 (mtt-85) REVERT: A 344 GLU cc_start: 0.8759 (tt0) cc_final: 0.8430 (tt0) REVERT: A 534 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8934 (tptm) REVERT: A 697 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.8847 (mtmm) REVERT: A 823 GLN cc_start: 0.8698 (mt0) cc_final: 0.8465 (mm-40) REVERT: B 534 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8978 (tptm) REVERT: B 823 GLN cc_start: 0.8810 (mt0) cc_final: 0.8601 (mt0) REVERT: C 149 HIS cc_start: 0.8784 (m-70) cc_final: 0.8409 (m-70) REVERT: C 224 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7884 (mtp85) REVERT: C 344 GLU cc_start: 0.8717 (tt0) cc_final: 0.8379 (tt0) REVERT: C 534 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8960 (tptm) REVERT: C 823 GLN cc_start: 0.8728 (mt0) cc_final: 0.8423 (mm-40) REVERT: H 40 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.6118 (ttm170) REVERT: I 40 ARG cc_start: 0.7762 (ttp-170) cc_final: 0.6258 (tpm170) REVERT: I 41 GLN cc_start: 0.7224 (tt0) cc_final: 0.7022 (tt0) REVERT: J 40 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.6138 (ttm170) REVERT: J 41 GLN cc_start: 0.7166 (tt0) cc_final: 0.6886 (tt0) outliers start: 24 outliers final: 15 residues processed: 263 average time/residue: 1.3244 time to fit residues: 410.7874 Evaluate side-chains 185 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain H residue 55 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 177 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 774 ASN B 149 HIS B 774 ASN B 883 GLN C 149 HIS C 489 GLN C 774 ASN C 883 GLN H 79 GLN H 103 ASN I 103 ASN J 79 GLN J 103 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.061953 restraints weight = 54254.690| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.22 r_work: 0.2733 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 27810 Z= 0.136 Angle : 0.648 8.452 38256 Z= 0.314 Chirality : 0.047 0.261 4803 Planarity : 0.004 0.044 4749 Dihedral : 11.779 65.171 6422 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.67 % Allowed : 5.75 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.54 (0.14), residues: 3513 helix: 1.44 (0.20), residues: 723 sheet: 0.42 (0.16), residues: 1026 loop : -0.04 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 38 HIS 0.006 0.001 HIS C 149 PHE 0.019 0.002 PHE B 930 TYR 0.024 0.001 TYR J 55 ARG 0.003 0.000 ARG C 322 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 63) link_NAG-ASN : angle 2.23718 ( 189) link_BETA1-4 : bond 0.00600 ( 60) link_BETA1-4 : angle 3.00650 ( 180) hydrogen bonds : bond 0.04345 ( 1177) hydrogen bonds : angle 5.25385 ( 3279) SS BOND : bond 0.00412 ( 45) SS BOND : angle 0.96309 ( 90) covalent geometry : bond 0.00294 (27642) covalent geometry : angle 0.59608 (37797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 3.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.6996 (p90) cc_final: 0.6750 (p90) REVERT: A 320 GLU cc_start: 0.8520 (tt0) cc_final: 0.8128 (tt0) REVERT: A 322 ARG cc_start: 0.8664 (mtt180) cc_final: 0.8200 (mtt180) REVERT: A 344 GLU cc_start: 0.8858 (tt0) cc_final: 0.8476 (tt0) REVERT: A 348 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7921 (mtp) REVERT: A 534 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8861 (tptm) REVERT: A 774 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7876 (t0) REVERT: A 823 GLN cc_start: 0.8618 (mt0) cc_final: 0.8393 (mm-40) REVERT: B 53 PHE cc_start: 0.7329 (p90) cc_final: 0.7098 (p90) REVERT: B 286 LYS cc_start: 0.8555 (ptmm) cc_final: 0.8161 (ptmm) REVERT: B 320 GLU cc_start: 0.8521 (tt0) cc_final: 0.8217 (tt0) REVERT: B 534 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8869 (tptm) REVERT: B 823 GLN cc_start: 0.8663 (mt0) cc_final: 0.8329 (mm-40) REVERT: C 167 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8423 (mm) REVERT: C 286 LYS cc_start: 0.8637 (ptmm) cc_final: 0.8300 (ptmm) REVERT: C 344 GLU cc_start: 0.8839 (tt0) cc_final: 0.8466 (tt0) REVERT: C 534 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8804 (tptp) REVERT: C 697 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9021 (mtmm) REVERT: C 823 GLN cc_start: 0.8676 (mt0) cc_final: 0.8384 (mm-40) REVERT: H 40 ARG cc_start: 0.7362 (ttp-170) cc_final: 0.5690 (ttm170) REVERT: I 40 ARG cc_start: 0.7505 (ttp-170) cc_final: 0.5626 (ttm170) REVERT: J 37 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8008 (m-40) REVERT: J 40 ARG cc_start: 0.7462 (ttp-170) cc_final: 0.5667 (ttm170) outliers start: 39 outliers final: 17 residues processed: 222 average time/residue: 1.4889 time to fit residues: 397.4053 Evaluate side-chains 187 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain J residue 37 ASN Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 99 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 242 optimal weight: 0.4980 chunk 167 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN C 489 GLN C 774 ASN C 961 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.062640 restraints weight = 54014.162| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.24 r_work: 0.2725 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27810 Z= 0.105 Angle : 0.555 8.896 38256 Z= 0.272 Chirality : 0.046 0.244 4803 Planarity : 0.003 0.044 4749 Dihedral : 7.896 54.228 6414 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.97 % Allowed : 6.44 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3513 helix: 2.07 (0.20), residues: 705 sheet: 0.54 (0.16), residues: 966 loop : 0.09 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 49 HIS 0.002 0.000 HIS A 421 PHE 0.024 0.001 PHE C 53 TYR 0.016 0.001 TYR J 54 ARG 0.009 0.000 ARG B 322 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 63) link_NAG-ASN : angle 1.79519 ( 189) link_BETA1-4 : bond 0.00595 ( 60) link_BETA1-4 : angle 2.53263 ( 180) hydrogen bonds : bond 0.03706 ( 1177) hydrogen bonds : angle 4.84935 ( 3279) SS BOND : bond 0.00228 ( 45) SS BOND : angle 0.76708 ( 90) covalent geometry : bond 0.00220 (27642) covalent geometry : angle 0.51405 (37797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7061 (p90) cc_final: 0.6848 (p90) REVERT: A 320 GLU cc_start: 0.8430 (tt0) cc_final: 0.7880 (tt0) REVERT: A 322 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8100 (mtt180) REVERT: A 344 GLU cc_start: 0.8871 (tt0) cc_final: 0.8525 (tt0) REVERT: A 534 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8784 (tptm) REVERT: A 823 GLN cc_start: 0.8630 (mt0) cc_final: 0.8383 (mm-40) REVERT: B 286 LYS cc_start: 0.8522 (ptmm) cc_final: 0.8146 (ptmm) REVERT: B 293 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7897 (mp10) REVERT: B 534 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8854 (tptm) REVERT: B 640 MET cc_start: 0.9191 (ttt) cc_final: 0.8967 (ttt) REVERT: B 697 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8857 (mtmm) REVERT: B 774 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7826 (t0) REVERT: B 823 GLN cc_start: 0.8644 (mt0) cc_final: 0.8342 (mm-40) REVERT: C 286 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8261 (ptmm) REVERT: C 344 GLU cc_start: 0.8889 (tt0) cc_final: 0.8536 (tt0) REVERT: C 534 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8766 (tptp) REVERT: C 697 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.9039 (mtmm) REVERT: C 774 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8089 (t0) REVERT: C 823 GLN cc_start: 0.8733 (mt0) cc_final: 0.8409 (mm-40) REVERT: H 40 ARG cc_start: 0.7385 (ttp-170) cc_final: 0.5762 (ttm170) REVERT: I 40 ARG cc_start: 0.7449 (ttp-170) cc_final: 0.5626 (ttm170) REVERT: J 31 SER cc_start: 0.9084 (t) cc_final: 0.8657 (t) REVERT: J 37 ASN cc_start: 0.8366 (m-40) cc_final: 0.8095 (m110) REVERT: J 40 ARG cc_start: 0.7513 (ttp-170) cc_final: 0.5744 (ttm170) outliers start: 46 outliers final: 17 residues processed: 224 average time/residue: 1.1305 time to fit residues: 305.0113 Evaluate side-chains 188 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 329 optimal weight: 30.0000 chunk 297 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 326 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 HIS A 774 ASN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 961 GLN C 627 HIS C 774 ASN C 824 GLN H 79 GLN L 71 ASN M 71 ASN N 71 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.084499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.058239 restraints weight = 54955.631| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.24 r_work: 0.2654 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 27810 Z= 0.301 Angle : 0.655 9.049 38256 Z= 0.323 Chirality : 0.048 0.264 4803 Planarity : 0.004 0.046 4749 Dihedral : 7.442 59.719 6414 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.23 % Allowed : 7.42 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3513 helix: 2.09 (0.20), residues: 696 sheet: 0.46 (0.16), residues: 1038 loop : 0.14 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 38 HIS 0.004 0.001 HIS C 126 PHE 0.029 0.002 PHE B 53 TYR 0.027 0.002 TYR L 51 ARG 0.003 0.001 ARG C 560 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 63) link_NAG-ASN : angle 1.97089 ( 189) link_BETA1-4 : bond 0.00544 ( 60) link_BETA1-4 : angle 2.58273 ( 180) hydrogen bonds : bond 0.04846 ( 1177) hydrogen bonds : angle 5.14745 ( 3279) SS BOND : bond 0.00588 ( 45) SS BOND : angle 1.10888 ( 90) covalent geometry : bond 0.00710 (27642) covalent geometry : angle 0.61626 (37797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.8339 (m-80) cc_final: 0.7972 (m-80) REVERT: A 320 GLU cc_start: 0.8411 (tt0) cc_final: 0.7654 (tt0) REVERT: A 322 ARG cc_start: 0.8812 (mtt180) cc_final: 0.7896 (mtt-85) REVERT: A 534 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8947 (tptm) REVERT: A 823 GLN cc_start: 0.8821 (mt0) cc_final: 0.8514 (mm-40) REVERT: B 286 LYS cc_start: 0.8536 (ptmm) cc_final: 0.8177 (ptmm) REVERT: B 534 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8953 (tptm) REVERT: B 697 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9084 (mtmm) REVERT: B 740 MET cc_start: 0.9530 (OUTLIER) cc_final: 0.9292 (mtt) REVERT: B 823 GLN cc_start: 0.8819 (mt0) cc_final: 0.8446 (mm-40) REVERT: C 286 LYS cc_start: 0.8639 (ptmm) cc_final: 0.8327 (ptmm) REVERT: C 534 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8919 (tptm) REVERT: C 823 GLN cc_start: 0.8816 (mt0) cc_final: 0.8464 (mm-40) REVERT: H 40 ARG cc_start: 0.7661 (ttp-170) cc_final: 0.5925 (tpm170) REVERT: I 40 ARG cc_start: 0.7661 (ttp-170) cc_final: 0.5799 (ttm170) REVERT: J 37 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8493 (m110) REVERT: J 40 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.5772 (tpm170) outliers start: 52 outliers final: 18 residues processed: 208 average time/residue: 1.3097 time to fit residues: 327.2398 Evaluate side-chains 184 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain J residue 37 ASN Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 141 optimal weight: 0.0970 chunk 157 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 GLN B 774 ASN B 840 GLN C 774 ASN C 824 GLN M 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.061411 restraints weight = 53996.929| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.22 r_work: 0.2724 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27810 Z= 0.095 Angle : 0.515 8.244 38256 Z= 0.259 Chirality : 0.044 0.300 4803 Planarity : 0.003 0.042 4749 Dihedral : 6.414 55.170 6408 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.54 % Allowed : 9.09 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3513 helix: 2.38 (0.20), residues: 705 sheet: 0.49 (0.16), residues: 1032 loop : 0.18 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 38 HIS 0.002 0.000 HIS B 126 PHE 0.030 0.001 PHE A 53 TYR 0.028 0.001 TYR J 55 ARG 0.002 0.000 ARG B 322 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 63) link_NAG-ASN : angle 1.57913 ( 189) link_BETA1-4 : bond 0.00493 ( 60) link_BETA1-4 : angle 2.04610 ( 180) hydrogen bonds : bond 0.03507 ( 1177) hydrogen bonds : angle 4.73938 ( 3279) SS BOND : bond 0.00379 ( 45) SS BOND : angle 0.84987 ( 90) covalent geometry : bond 0.00199 (27642) covalent geometry : angle 0.48377 (37797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.8321 (m-80) cc_final: 0.7915 (m-80) REVERT: A 534 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8897 (tptm) REVERT: A 774 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8053 (t0) REVERT: A 823 GLN cc_start: 0.8758 (mt0) cc_final: 0.8464 (mm-40) REVERT: B 286 LYS cc_start: 0.8514 (ptmm) cc_final: 0.8172 (ptmm) REVERT: B 534 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8910 (tptm) REVERT: B 774 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8281 (t0) REVERT: B 823 GLN cc_start: 0.8759 (mt0) cc_final: 0.8419 (mm-40) REVERT: C 286 LYS cc_start: 0.8493 (ptmm) cc_final: 0.8137 (ptmm) REVERT: C 534 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8914 (tptm) REVERT: C 823 GLN cc_start: 0.8796 (mt0) cc_final: 0.8434 (mm-40) REVERT: H 40 ARG cc_start: 0.7563 (ttp-170) cc_final: 0.5903 (tpm170) REVERT: I 40 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.5818 (ttm170) REVERT: J 37 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8171 (m110) REVERT: J 40 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.5728 (tpm170) outliers start: 36 outliers final: 19 residues processed: 201 average time/residue: 1.2332 time to fit residues: 295.1210 Evaluate side-chains 184 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain J residue 37 ASN Chi-restraints excluded: chain N residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 961 GLN B 840 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.060246 restraints weight = 54489.241| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.24 r_work: 0.2700 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 27810 Z= 0.154 Angle : 0.530 8.121 38256 Z= 0.265 Chirality : 0.044 0.241 4803 Planarity : 0.003 0.041 4749 Dihedral : 6.267 57.724 6404 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.63 % Allowed : 9.35 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.01 (0.14), residues: 3513 helix: 2.44 (0.20), residues: 705 sheet: 0.46 (0.16), residues: 1017 loop : 0.17 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 36 HIS 0.002 0.001 HIS C 126 PHE 0.029 0.001 PHE B 53 TYR 0.030 0.001 TYR I 55 ARG 0.002 0.000 ARG B 891 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 63) link_NAG-ASN : angle 1.57405 ( 189) link_BETA1-4 : bond 0.00436 ( 60) link_BETA1-4 : angle 2.09711 ( 180) hydrogen bonds : bond 0.03739 ( 1177) hydrogen bonds : angle 4.74143 ( 3279) SS BOND : bond 0.00303 ( 45) SS BOND : angle 0.95279 ( 90) covalent geometry : bond 0.00356 (27642) covalent geometry : angle 0.49841 (37797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.8338 (m-80) cc_final: 0.7974 (m-80) REVERT: A 534 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8889 (tptm) REVERT: A 774 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8146 (t0) REVERT: A 823 GLN cc_start: 0.8793 (mt0) cc_final: 0.8497 (mm-40) REVERT: B 286 LYS cc_start: 0.8525 (ptmm) cc_final: 0.8176 (ptmm) REVERT: B 534 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8933 (tptm) REVERT: B 823 GLN cc_start: 0.8807 (mt0) cc_final: 0.8416 (mm-40) REVERT: C 286 LYS cc_start: 0.8572 (ptmm) cc_final: 0.8258 (ptmm) REVERT: C 534 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8930 (tptm) REVERT: C 823 GLN cc_start: 0.8817 (mt0) cc_final: 0.8466 (mm-40) REVERT: H 40 ARG cc_start: 0.7580 (ttp-170) cc_final: 0.5905 (tpm170) REVERT: I 40 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.5858 (tpm170) REVERT: J 37 ASN cc_start: 0.8552 (m-40) cc_final: 0.8269 (m110) outliers start: 38 outliers final: 20 residues processed: 191 average time/residue: 1.6022 time to fit residues: 367.9445 Evaluate side-chains 179 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain J residue 55 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 163 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 312 optimal weight: 9.9990 chunk 246 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 198 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.087331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.061312 restraints weight = 54294.755| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.24 r_work: 0.2723 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27810 Z= 0.101 Angle : 0.499 7.721 38256 Z= 0.252 Chirality : 0.043 0.230 4803 Planarity : 0.003 0.040 4749 Dihedral : 5.980 58.981 6404 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.50 % Allowed : 9.78 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.99 (0.14), residues: 3513 helix: 2.53 (0.20), residues: 705 sheet: 0.49 (0.17), residues: 933 loop : 0.09 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 36 HIS 0.002 0.000 HIS B 126 PHE 0.029 0.001 PHE B 53 TYR 0.039 0.001 TYR J 55 ARG 0.002 0.000 ARG B 891 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 63) link_NAG-ASN : angle 1.43799 ( 189) link_BETA1-4 : bond 0.00460 ( 60) link_BETA1-4 : angle 1.95202 ( 180) hydrogen bonds : bond 0.03377 ( 1177) hydrogen bonds : angle 4.62154 ( 3279) SS BOND : bond 0.00236 ( 45) SS BOND : angle 0.99992 ( 90) covalent geometry : bond 0.00219 (27642) covalent geometry : angle 0.47074 (37797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.8268 (m-80) cc_final: 0.7874 (m-80) REVERT: A 320 GLU cc_start: 0.8351 (tt0) cc_final: 0.8109 (tt0) REVERT: A 534 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8873 (tptm) REVERT: A 774 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8025 (t0) REVERT: A 823 GLN cc_start: 0.8783 (mt0) cc_final: 0.8468 (mm-40) REVERT: B 286 LYS cc_start: 0.8505 (ptmm) cc_final: 0.8153 (ptmm) REVERT: B 534 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8913 (tptm) REVERT: B 740 MET cc_start: 0.9506 (OUTLIER) cc_final: 0.9236 (mtt) REVERT: B 823 GLN cc_start: 0.8772 (mt0) cc_final: 0.8407 (mm-40) REVERT: B 824 GLN cc_start: 0.8630 (pt0) cc_final: 0.8206 (tt0) REVERT: C 286 LYS cc_start: 0.8498 (ptmm) cc_final: 0.8170 (ptmm) REVERT: C 534 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8914 (tptm) REVERT: C 823 GLN cc_start: 0.8809 (mt0) cc_final: 0.8516 (mm-40) REVERT: C 824 GLN cc_start: 0.8647 (pt0) cc_final: 0.8215 (pm20) REVERT: H 40 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.5878 (tpm170) REVERT: I 40 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.5796 (tpm170) REVERT: J 37 ASN cc_start: 0.8461 (m-40) cc_final: 0.8158 (m110) REVERT: J 40 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.5749 (ttm170) outliers start: 35 outliers final: 22 residues processed: 184 average time/residue: 1.1767 time to fit residues: 259.9949 Evaluate side-chains 182 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 969 PHE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 969 PHE Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain I residue 37 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 15 optimal weight: 4.9990 chunk 316 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 335 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 347 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 ASN B 840 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.058918 restraints weight = 54533.850| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.22 r_work: 0.2646 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 27810 Z= 0.259 Angle : 0.586 7.824 38256 Z= 0.291 Chirality : 0.046 0.253 4803 Planarity : 0.004 0.042 4749 Dihedral : 6.380 59.863 6404 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.46 % Allowed : 10.08 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.03 (0.14), residues: 3513 helix: 2.47 (0.20), residues: 696 sheet: 0.50 (0.16), residues: 1035 loop : 0.16 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 38 HIS 0.003 0.001 HIS C 126 PHE 0.030 0.002 PHE B 53 TYR 0.026 0.002 TYR I 55 ARG 0.004 0.001 ARG C 560 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 63) link_NAG-ASN : angle 1.67712 ( 189) link_BETA1-4 : bond 0.00442 ( 60) link_BETA1-4 : angle 2.12876 ( 180) hydrogen bonds : bond 0.04300 ( 1177) hydrogen bonds : angle 4.86230 ( 3279) SS BOND : bond 0.00526 ( 45) SS BOND : angle 1.36096 ( 90) covalent geometry : bond 0.00607 (27642) covalent geometry : angle 0.55421 (37797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.8336 (m-80) cc_final: 0.8004 (m-80) REVERT: A 320 GLU cc_start: 0.8313 (tt0) cc_final: 0.8044 (tt0) REVERT: A 534 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8950 (tptm) REVERT: A 774 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8319 (t0) REVERT: A 823 GLN cc_start: 0.8857 (mt0) cc_final: 0.8530 (mm-40) REVERT: B 286 LYS cc_start: 0.8595 (ptmm) cc_final: 0.8251 (ptmm) REVERT: B 534 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8962 (tptm) REVERT: B 823 GLN cc_start: 0.8810 (mt0) cc_final: 0.8442 (mm-40) REVERT: B 824 GLN cc_start: 0.8659 (pt0) cc_final: 0.8208 (tt0) REVERT: C 286 LYS cc_start: 0.8646 (ptmm) cc_final: 0.8347 (ptmm) REVERT: C 534 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8920 (tptm) REVERT: C 823 GLN cc_start: 0.8830 (mt0) cc_final: 0.8481 (mm-40) REVERT: H 40 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.5859 (tpm170) REVERT: I 40 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.5912 (tpm170) REVERT: J 37 ASN cc_start: 0.8646 (m-40) cc_final: 0.8365 (m110) REVERT: J 40 ARG cc_start: 0.7575 (ttp-170) cc_final: 0.5766 (ttm170) outliers start: 34 outliers final: 20 residues processed: 180 average time/residue: 1.1238 time to fit residues: 243.8609 Evaluate side-chains 174 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 298 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 192 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 194 optimal weight: 0.0980 chunk 287 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 312 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.087010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060966 restraints weight = 54235.291| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.28 r_work: 0.2689 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27810 Z= 0.109 Angle : 0.499 7.377 38256 Z= 0.252 Chirality : 0.043 0.231 4803 Planarity : 0.003 0.041 4749 Dihedral : 5.893 59.696 6404 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.03 % Allowed : 10.77 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.06 (0.14), residues: 3513 helix: 2.50 (0.20), residues: 705 sheet: 0.52 (0.16), residues: 1035 loop : 0.17 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 38 HIS 0.002 0.000 HIS A 315 PHE 0.029 0.001 PHE B 53 TYR 0.026 0.001 TYR I 55 ARG 0.003 0.000 ARG A 322 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 63) link_NAG-ASN : angle 1.41074 ( 189) link_BETA1-4 : bond 0.00453 ( 60) link_BETA1-4 : angle 1.86034 ( 180) hydrogen bonds : bond 0.03410 ( 1177) hydrogen bonds : angle 4.60973 ( 3279) SS BOND : bond 0.00262 ( 45) SS BOND : angle 1.14739 ( 90) covalent geometry : bond 0.00243 (27642) covalent geometry : angle 0.47134 (37797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.8332 (m-80) cc_final: 0.7979 (m-80) REVERT: A 320 GLU cc_start: 0.8367 (tt0) cc_final: 0.8103 (tt0) REVERT: A 534 LYS cc_start: 0.9273 (ptpp) cc_final: 0.8907 (tptm) REVERT: A 774 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8129 (t0) REVERT: A 823 GLN cc_start: 0.8793 (mt0) cc_final: 0.8495 (mm-40) REVERT: B 286 LYS cc_start: 0.8530 (ptmm) cc_final: 0.8201 (ptmt) REVERT: B 534 LYS cc_start: 0.9325 (ptpp) cc_final: 0.8917 (tptm) REVERT: B 823 GLN cc_start: 0.8771 (mt0) cc_final: 0.8432 (mm-40) REVERT: B 824 GLN cc_start: 0.8663 (pt0) cc_final: 0.8144 (tt0) REVERT: C 286 LYS cc_start: 0.8512 (ptmm) cc_final: 0.8197 (ptmt) REVERT: C 534 LYS cc_start: 0.9304 (ptpp) cc_final: 0.8947 (tptm) REVERT: C 740 MET cc_start: 0.9489 (mtt) cc_final: 0.9239 (mtt) REVERT: C 823 GLN cc_start: 0.8819 (mt0) cc_final: 0.8486 (mm-40) REVERT: H 40 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.5879 (ttm170) REVERT: I 40 ARG cc_start: 0.7502 (ttp-170) cc_final: 0.5883 (tpm170) REVERT: J 37 ASN cc_start: 0.8498 (m-40) cc_final: 0.8199 (m110) REVERT: J 40 ARG cc_start: 0.7547 (ttp-170) cc_final: 0.5777 (ttm170) outliers start: 24 outliers final: 18 residues processed: 184 average time/residue: 1.2524 time to fit residues: 275.2217 Evaluate side-chains 173 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 119 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 214 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 ASN B 840 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.060304 restraints weight = 53979.250| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.26 r_work: 0.2675 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27810 Z= 0.142 Angle : 0.512 7.272 38256 Z= 0.258 Chirality : 0.044 0.235 4803 Planarity : 0.003 0.040 4749 Dihedral : 5.841 59.440 6392 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.90 % Allowed : 11.07 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 1.05 (0.14), residues: 3513 helix: 2.55 (0.20), residues: 705 sheet: 0.52 (0.16), residues: 966 loop : 0.14 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 38 HIS 0.002 0.001 HIS B 126 PHE 0.029 0.001 PHE B 53 TYR 0.026 0.001 TYR I 55 ARG 0.006 0.000 ARG B 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 63) link_NAG-ASN : angle 1.45956 ( 189) link_BETA1-4 : bond 0.00426 ( 60) link_BETA1-4 : angle 1.91038 ( 180) hydrogen bonds : bond 0.03629 ( 1177) hydrogen bonds : angle 4.60386 ( 3279) SS BOND : bond 0.00294 ( 45) SS BOND : angle 1.28686 ( 90) covalent geometry : bond 0.00330 (27642) covalent geometry : angle 0.48344 (37797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.8344 (m-80) cc_final: 0.7988 (m-80) REVERT: A 320 GLU cc_start: 0.8333 (tt0) cc_final: 0.8084 (tt0) REVERT: A 534 LYS cc_start: 0.9295 (ptpp) cc_final: 0.8912 (tptm) REVERT: A 774 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8209 (t0) REVERT: A 823 GLN cc_start: 0.8824 (mt0) cc_final: 0.8525 (mm-40) REVERT: B 286 LYS cc_start: 0.8530 (ptmm) cc_final: 0.8198 (ptmt) REVERT: B 534 LYS cc_start: 0.9341 (ptpp) cc_final: 0.8928 (tptm) REVERT: B 823 GLN cc_start: 0.8779 (mt0) cc_final: 0.8436 (mm-40) REVERT: C 286 LYS cc_start: 0.8527 (ptmm) cc_final: 0.8224 (ptmt) REVERT: C 534 LYS cc_start: 0.9319 (ptpp) cc_final: 0.8948 (tptm) REVERT: C 740 MET cc_start: 0.9500 (mtt) cc_final: 0.9275 (mtt) REVERT: C 823 GLN cc_start: 0.8831 (mt0) cc_final: 0.8493 (mm-40) REVERT: H 40 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.5835 (ttm170) REVERT: H 48 GLU cc_start: 0.8614 (tt0) cc_final: 0.8405 (tt0) REVERT: I 40 ARG cc_start: 0.7544 (ttp-170) cc_final: 0.5877 (tpm170) REVERT: J 37 ASN cc_start: 0.8517 (m-40) cc_final: 0.8225 (m110) REVERT: J 40 ARG cc_start: 0.7584 (ttp-170) cc_final: 0.5791 (ttm170) outliers start: 21 outliers final: 19 residues processed: 179 average time/residue: 1.2065 time to fit residues: 258.3485 Evaluate side-chains 173 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 545 CYS Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 545 CYS Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 20.0000 chunk 298 optimal weight: 0.3980 chunk 137 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 ASN B 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.057491 restraints weight = 54678.685| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.26 r_work: 0.2630 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 27810 Z= 0.275 Angle : 0.607 7.483 38256 Z= 0.302 Chirality : 0.046 0.252 4803 Planarity : 0.004 0.042 4749 Dihedral : 6.331 59.431 6392 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.07 % Allowed : 11.07 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.93 (0.14), residues: 3513 helix: 2.44 (0.20), residues: 696 sheet: 0.39 (0.16), residues: 1035 loop : 0.10 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 38 HIS 0.003 0.001 HIS C 126 PHE 0.029 0.002 PHE A 53 TYR 0.027 0.002 TYR H 55 ARG 0.007 0.001 ARG B 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 63) link_NAG-ASN : angle 1.71273 ( 189) link_BETA1-4 : bond 0.00431 ( 60) link_BETA1-4 : angle 2.08067 ( 180) hydrogen bonds : bond 0.04475 ( 1177) hydrogen bonds : angle 4.87564 ( 3279) SS BOND : bond 0.00485 ( 45) SS BOND : angle 1.49602 ( 90) covalent geometry : bond 0.00651 (27642) covalent geometry : angle 0.57674 (37797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15010.65 seconds wall clock time: 265 minutes 30.62 seconds (15930.62 seconds total)