Starting phenix.real_space_refine on Wed Nov 19 20:05:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dez_46804/11_2025/9dez_46804.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dez_46804/11_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_46804/11_2025/9dez_46804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dez_46804/11_2025/9dez_46804.map" model { file = "/net/cci-nas-00/data/ceres_data/9dez_46804/11_2025/9dez_46804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dez_46804/11_2025/9dez_46804.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'ASN:plan1': 8, 'HIS:plan': 2, 'GLU:plan': 11, 'ASP:plan': 10, 'ARG:plan': 2, 'GLN:plan1': 1} 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: {'ASN:plan1': 8, 'HIS:plan': 2, 'GLU:plan': 11, 'ASP:plan': 10, 'ARG:plan': 2, 'GLN:plan1': 1} 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: {'ASN:plan1': 8, 'HIS:plan': 2, 'GLU:plan': 11, 'ASP:plan': 10, 'ARG:plan': 2, 'GLN:plan1': 1} 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, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2} 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, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2} 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, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2} 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, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE: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, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE: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, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE: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: 7.14, per 1000 atoms: 0.26 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: 2.91 Conformation dependent library (CDL) restraints added in 1.2 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: 1.60 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: 7.48 Time building geometry restraints manager: 3.68 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: 0.06 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.560 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (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 ARG 0.005 0.001 ARG C 272 TYR 0.039 0.003 TYR M 51 PHE 0.031 0.004 PHE B 930 TRP 0.019 0.002 TRP I 108 HIS 0.006 0.002 HIS A 933 Details of bonding type rmsd covalent geometry : bond 0.00643 (27642) covalent geometry : angle 0.86648 (37797) SS BOND : bond 0.00643 ( 45) SS BOND : angle 1.28176 ( 90) hydrogen bonds : bond 0.14750 ( 1177) hydrogen bonds : angle 7.30612 ( 3279) link_BETA1-4 : bond 0.01629 ( 60) link_BETA1-4 : angle 3.80912 ( 180) link_NAG-ASN : bond 0.00915 ( 63) link_NAG-ASN : angle 3.80220 ( 189) *********************** 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 : 1.078 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 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: 0.6504 time to fit residues: 200.1361 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 : 1.041 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 774 ASN C 149 HIS C 489 GLN C 774 ASN C 883 GLN H 79 GLN H 103 ASN I 37 ASN I 103 ASN J 79 GLN J 103 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.062411 restraints weight = 54463.053| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.24 r_work: 0.2742 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1513 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= 0.125 Angle : 0.644 8.338 38256 Z= 0.313 Chirality : 0.047 0.260 4803 Planarity : 0.004 0.044 4749 Dihedral : 11.571 64.320 6422 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3513 helix: 1.43 (0.20), residues: 723 sheet: 0.48 (0.16), residues: 1017 loop : -0.03 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 891 TYR 0.023 0.001 TYR J 55 PHE 0.018 0.002 PHE B 930 TRP 0.015 0.002 TRP I 38 HIS 0.005 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00257 (27642) covalent geometry : angle 0.59375 (37797) SS BOND : bond 0.00327 ( 45) SS BOND : angle 0.97763 ( 90) hydrogen bonds : bond 0.04401 ( 1177) hydrogen bonds : angle 5.25771 ( 3279) link_BETA1-4 : bond 0.00521 ( 60) link_BETA1-4 : angle 2.94943 ( 180) link_NAG-ASN : bond 0.00499 ( 63) link_NAG-ASN : angle 2.17679 ( 189) *********************** 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 232 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.904 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 53 PHE cc_start: 0.7034 (p90) cc_final: 0.6786 (p90) REVERT: A 344 GLU cc_start: 0.8885 (tt0) cc_final: 0.8532 (tt0) REVERT: A 348 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7941 (mtp) REVERT: A 534 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8829 (tptp) REVERT: A 774 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7885 (t0) REVERT: A 823 GLN cc_start: 0.8606 (mt0) cc_final: 0.8390 (mm-40) REVERT: B 53 PHE cc_start: 0.7325 (p90) cc_final: 0.7110 (p90) REVERT: B 286 LYS cc_start: 0.8573 (ptmm) cc_final: 0.8173 (ptmm) REVERT: B 322 ARG cc_start: 0.8810 (mtp85) cc_final: 0.8572 (mtt90) REVERT: B 534 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8868 (tptm) REVERT: B 823 GLN cc_start: 0.8660 (mt0) cc_final: 0.8351 (mm-40) REVERT: C 167 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8460 (mm) REVERT: C 286 LYS cc_start: 0.8650 (ptmm) cc_final: 0.8306 (ptmm) REVERT: C 344 GLU cc_start: 0.8848 (tt0) cc_final: 0.8512 (tt0) REVERT: C 534 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8813 (tptp) REVERT: C 697 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9079 (mtmm) REVERT: C 823 GLN cc_start: 0.8674 (mt0) cc_final: 0.8434 (mm-40) REVERT: H 40 ARG cc_start: 0.7359 (ttp-170) cc_final: 0.5674 (ttm170) REVERT: I 40 ARG cc_start: 0.7530 (ttp-170) cc_final: 0.5622 (ttm170) REVERT: J 37 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8034 (m-40) REVERT: J 40 ARG cc_start: 0.7501 (ttp-170) cc_final: 0.5642 (ttm170) outliers start: 39 outliers final: 16 residues processed: 222 average time/residue: 0.6002 time to fit residues: 158.1463 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 : 1.059 ------------------------------------------------------------------------------- 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 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 249 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 B 883 GLN C 489 GLN C 774 ASN I 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.061913 restraints weight = 54398.161| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.24 r_work: 0.2709 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27810 Z= 0.125 Angle : 0.578 9.009 38256 Z= 0.282 Chirality : 0.046 0.249 4803 Planarity : 0.004 0.044 4749 Dihedral : 8.369 54.604 6412 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.97 % Allowed : 6.56 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3513 helix: 2.02 (0.20), residues: 705 sheet: 0.49 (0.16), residues: 1050 loop : 0.20 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 891 TYR 0.020 0.001 TYR J 54 PHE 0.026 0.001 PHE C 53 TRP 0.012 0.001 TRP I 36 HIS 0.002 0.000 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00278 (27642) covalent geometry : angle 0.53497 (37797) SS BOND : bond 0.00259 ( 45) SS BOND : angle 0.83021 ( 90) hydrogen bonds : bond 0.03966 ( 1177) hydrogen bonds : angle 4.93948 ( 3279) link_BETA1-4 : bond 0.00553 ( 60) link_BETA1-4 : angle 2.62966 ( 180) link_NAG-ASN : bond 0.00421 ( 63) link_NAG-ASN : angle 1.89214 ( 189) *********************** 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 226 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 1.069 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: 0.7082 (p90) cc_final: 0.6851 (p90) REVERT: A 344 GLU cc_start: 0.8859 (tt0) cc_final: 0.8507 (tt0) REVERT: A 534 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8855 (tptm) REVERT: A 823 GLN cc_start: 0.8649 (mt0) cc_final: 0.8411 (mm-40) REVERT: B 53 PHE cc_start: 0.7408 (p90) cc_final: 0.7205 (p90) REVERT: B 286 LYS cc_start: 0.8556 (ptmm) cc_final: 0.8178 (ptmm) REVERT: B 322 ARG cc_start: 0.8750 (mtp85) cc_final: 0.8437 (mtt90) REVERT: B 534 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8872 (tptm) REVERT: B 640 MET cc_start: 0.9199 (ttt) cc_final: 0.8992 (ttt) REVERT: B 823 GLN cc_start: 0.8669 (mt0) cc_final: 0.8323 (mm-40) REVERT: C 286 LYS cc_start: 0.8629 (ptmm) cc_final: 0.8313 (ptmm) REVERT: C 320 GLU cc_start: 0.8692 (tt0) cc_final: 0.8378 (pp20) REVERT: C 344 GLU cc_start: 0.8891 (tt0) cc_final: 0.8492 (tt0) REVERT: C 534 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8775 (tptp) REVERT: C 697 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9023 (mtmm) REVERT: C 823 GLN cc_start: 0.8739 (mt0) cc_final: 0.8412 (mm-40) REVERT: H 40 ARG cc_start: 0.7429 (ttp-170) cc_final: 0.5733 (ttm170) REVERT: I 40 ARG cc_start: 0.7466 (ttp-170) cc_final: 0.5646 (ttm170) REVERT: J 37 ASN cc_start: 0.8382 (m-40) cc_final: 0.8132 (m110) REVERT: J 40 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.5715 (ttm170) outliers start: 46 outliers final: 16 residues processed: 218 average time/residue: 0.6005 time to fit residues: 155.5165 Evaluate side-chains 182 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 47 LEU Chi-restraints excluded: chain J residue 55 TYR 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 338 optimal weight: 7.9990 chunk 179 optimal weight: 0.5980 chunk 288 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 345 optimal weight: 40.0000 chunk 74 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 chunk 308 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN B 774 ASN B 961 GLN C 627 HIS C 774 ASN C 824 GLN C 961 GLN H 79 GLN L 71 ASN M 71 ASN N 71 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059116 restraints weight = 54695.063| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.25 r_work: 0.2674 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27810 Z= 0.222 Angle : 0.601 8.854 38256 Z= 0.299 Chirality : 0.047 0.254 4803 Planarity : 0.004 0.045 4749 Dihedral : 7.077 59.696 6410 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.02 % Allowed : 7.25 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.14), residues: 3513 helix: 2.24 (0.20), residues: 696 sheet: 0.56 (0.16), residues: 1011 loop : 0.17 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 891 TYR 0.023 0.002 TYR I 55 PHE 0.025 0.001 PHE C 53 TRP 0.008 0.001 TRP J 108 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00521 (27642) covalent geometry : angle 0.56345 (37797) SS BOND : bond 0.00504 ( 45) SS BOND : angle 0.96470 ( 90) hydrogen bonds : bond 0.04445 ( 1177) hydrogen bonds : angle 5.01966 ( 3279) link_BETA1-4 : bond 0.00473 ( 60) link_BETA1-4 : angle 2.44791 ( 180) link_NAG-ASN : bond 0.00423 ( 63) link_NAG-ASN : angle 1.85727 ( 189) *********************** 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 224 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 1.055 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: 0.8332 (m-80) cc_final: 0.7945 (m-80) REVERT: A 534 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8936 (tptm) REVERT: A 774 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8119 (t0) REVERT: A 823 GLN cc_start: 0.8810 (mt0) cc_final: 0.8507 (mm-40) REVERT: B 286 LYS cc_start: 0.8553 (ptmm) cc_final: 0.8192 (ptmm) REVERT: B 320 GLU cc_start: 0.8481 (tt0) cc_final: 0.8229 (tt0) REVERT: B 322 ARG cc_start: 0.8866 (mtp85) cc_final: 0.8376 (mtt90) REVERT: B 534 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8950 (tptm) REVERT: B 823 GLN cc_start: 0.8833 (mt0) cc_final: 0.8467 (mm-40) REVERT: C 286 LYS cc_start: 0.8600 (ptmm) cc_final: 0.8277 (ptmm) REVERT: C 534 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8906 (tptp) REVERT: C 823 GLN cc_start: 0.8795 (mt0) cc_final: 0.8470 (mm-40) REVERT: H 40 ARG cc_start: 0.7625 (ttp-170) cc_final: 0.5915 (tpm170) REVERT: J 37 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8466 (m110) REVERT: J 40 ARG cc_start: 0.7536 (ttp-170) cc_final: 0.5725 (tpm170) outliers start: 47 outliers final: 20 residues processed: 211 average time/residue: 0.5967 time to fit residues: 149.7423 Evaluate side-chains 185 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 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 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 M residue 71 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 171 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 317 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 329 optimal weight: 40.0000 chunk 179 optimal weight: 0.7980 chunk 234 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN A 895 GLN B 774 ASN C 774 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.061075 restraints weight = 54091.855| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.24 r_work: 0.2716 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27810 Z= 0.106 Angle : 0.521 8.250 38256 Z= 0.262 Chirality : 0.044 0.240 4803 Planarity : 0.003 0.043 4749 Dihedral : 6.404 59.832 6402 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.59 % Allowed : 9.01 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3513 helix: 2.37 (0.20), residues: 705 sheet: 0.56 (0.16), residues: 1008 loop : 0.19 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.023 0.001 TYR I 55 PHE 0.029 0.001 PHE B 53 TRP 0.006 0.001 TRP J 49 HIS 0.002 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00227 (27642) covalent geometry : angle 0.48876 (37797) SS BOND : bond 0.00255 ( 45) SS BOND : angle 0.90929 ( 90) hydrogen bonds : bond 0.03588 ( 1177) hydrogen bonds : angle 4.75560 ( 3279) link_BETA1-4 : bond 0.00472 ( 60) link_BETA1-4 : angle 2.08770 ( 180) link_NAG-ASN : bond 0.00355 ( 63) link_NAG-ASN : angle 1.60324 ( 189) *********************** 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 212 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 1.126 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: 0.8322 (m-80) cc_final: 0.7953 (m-80) REVERT: A 322 ARG cc_start: 0.8738 (mtp180) cc_final: 0.8236 (mtt-85) REVERT: A 534 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8909 (tptm) REVERT: A 823 GLN cc_start: 0.8747 (mt0) cc_final: 0.8461 (mm-40) REVERT: B 286 LYS cc_start: 0.8506 (ptmm) cc_final: 0.8155 (ptmm) REVERT: B 320 GLU cc_start: 0.8449 (tt0) cc_final: 0.8192 (tt0) REVERT: B 322 ARG cc_start: 0.8835 (mtp85) cc_final: 0.8348 (mtt90) REVERT: B 534 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8919 (tptm) REVERT: B 823 GLN cc_start: 0.8771 (mt0) cc_final: 0.8435 (mm-40) REVERT: C 286 LYS cc_start: 0.8520 (ptmm) cc_final: 0.8170 (ptmm) REVERT: C 534 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8914 (tptm) REVERT: C 823 GLN cc_start: 0.8798 (mt0) cc_final: 0.8528 (mm-40) REVERT: C 824 GLN cc_start: 0.8655 (pt0) cc_final: 0.8237 (pm20) REVERT: H 40 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.5905 (tpm170) REVERT: I 40 ARG cc_start: 0.7589 (ttp-170) cc_final: 0.5831 (ttm170) REVERT: J 37 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8231 (m110) REVERT: J 40 ARG cc_start: 0.7530 (ttp-170) cc_final: 0.5727 (tpm170) outliers start: 37 outliers final: 17 residues processed: 202 average time/residue: 0.6173 time to fit residues: 147.6615 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 : 1.007 ------------------------------------------------------------------------------- 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 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 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 55 TYR Chi-restraints excluded: chain J residue 37 ASN Chi-restraints excluded: chain J residue 55 TYR 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 333 optimal weight: 0.6980 chunk 234 optimal weight: 0.5980 chunk 226 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 286 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN A 961 GLN B 774 ASN B 840 GLN C 774 ASN H 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.060262 restraints weight = 54461.683| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.25 r_work: 0.2701 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27810 Z= 0.150 Angle : 0.527 8.100 38256 Z= 0.264 Chirality : 0.044 0.240 4803 Planarity : 0.003 0.042 4749 Dihedral : 6.223 57.586 6402 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.89 % Allowed : 9.01 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3513 helix: 2.43 (0.20), residues: 705 sheet: 0.56 (0.16), residues: 993 loop : 0.16 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 322 TYR 0.031 0.001 TYR J 55 PHE 0.028 0.001 PHE A 53 TRP 0.007 0.001 TRP J 49 HIS 0.002 0.000 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00349 (27642) covalent geometry : angle 0.49536 (37797) SS BOND : bond 0.00335 ( 45) SS BOND : angle 0.97278 ( 90) hydrogen bonds : bond 0.03731 ( 1177) hydrogen bonds : angle 4.73520 ( 3279) link_BETA1-4 : bond 0.00443 ( 60) link_BETA1-4 : angle 2.08766 ( 180) link_NAG-ASN : bond 0.00341 ( 63) link_NAG-ASN : angle 1.56972 ( 189) *********************** 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 211 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 1.066 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: 0.8347 (m-80) cc_final: 0.7978 (m-80) REVERT: A 534 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8894 (tptm) REVERT: A 823 GLN cc_start: 0.8782 (mt0) cc_final: 0.8484 (mm-40) REVERT: B 286 LYS cc_start: 0.8526 (ptmm) cc_final: 0.8177 (ptmm) REVERT: B 320 GLU cc_start: 0.8398 (tt0) cc_final: 0.8137 (tt0) REVERT: B 322 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8342 (mtt90) REVERT: B 534 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8942 (tptm) REVERT: B 740 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9254 (mtt) REVERT: B 823 GLN cc_start: 0.8801 (mt0) cc_final: 0.8414 (mm-40) REVERT: C 286 LYS cc_start: 0.8555 (ptmm) cc_final: 0.8239 (ptmm) REVERT: C 534 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8936 (tptm) REVERT: C 823 GLN cc_start: 0.8824 (mt0) cc_final: 0.8490 (mm-40) REVERT: I 40 ARG cc_start: 0.7620 (ttp-170) cc_final: 0.5856 (tpm170) REVERT: J 37 ASN cc_start: 0.8564 (m-40) cc_final: 0.8279 (m110) REVERT: J 40 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.5753 (tpm170) outliers start: 44 outliers final: 21 residues processed: 198 average time/residue: 0.6375 time to fit residues: 148.9791 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 : 0.969 ------------------------------------------------------------------------------- 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 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 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 H residue 55 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 154 optimal weight: 0.9990 chunk 338 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 234 optimal weight: 0.8980 chunk 341 optimal weight: 6.9990 chunk 100 optimal weight: 0.0020 chunk 294 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 306 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN B 774 ASN B 840 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.061436 restraints weight = 54000.192| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.23 r_work: 0.2726 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27810 Z= 0.097 Angle : 0.498 7.701 38256 Z= 0.252 Chirality : 0.044 0.313 4803 Planarity : 0.003 0.040 4749 Dihedral : 5.935 58.883 6402 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.37 % Allowed : 9.78 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.14), residues: 3513 helix: 2.52 (0.20), residues: 705 sheet: 0.50 (0.17), residues: 930 loop : 0.13 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 322 TYR 0.023 0.001 TYR H 55 PHE 0.028 0.001 PHE B 53 TRP 0.005 0.001 TRP I 49 HIS 0.002 0.000 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00209 (27642) covalent geometry : angle 0.46942 (37797) SS BOND : bond 0.00189 ( 45) SS BOND : angle 1.00866 ( 90) hydrogen bonds : bond 0.03352 ( 1177) hydrogen bonds : angle 4.61604 ( 3279) link_BETA1-4 : bond 0.00458 ( 60) link_BETA1-4 : angle 1.94274 ( 180) link_NAG-ASN : bond 0.00317 ( 63) link_NAG-ASN : angle 1.43757 ( 189) *********************** 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 196 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.119 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: 0.8270 (m-80) cc_final: 0.7878 (m-80) REVERT: A 322 ARG cc_start: 0.8684 (mtp180) cc_final: 0.8181 (mtt-85) REVERT: A 534 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8871 (tptm) REVERT: A 774 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7921 (t0) REVERT: A 823 GLN cc_start: 0.8789 (mt0) cc_final: 0.8467 (mm-40) REVERT: B 286 LYS cc_start: 0.8503 (ptmm) cc_final: 0.8148 (ptmm) REVERT: B 320 GLU cc_start: 0.8351 (tt0) cc_final: 0.8070 (tt0) REVERT: B 322 ARG cc_start: 0.8795 (mtp85) cc_final: 0.8300 (mtt90) REVERT: B 534 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8941 (tptm) REVERT: B 774 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7917 (t0) REVERT: B 823 GLN cc_start: 0.8759 (mt0) cc_final: 0.8363 (mm-40) REVERT: B 824 GLN cc_start: 0.8624 (pt0) cc_final: 0.8195 (tt0) REVERT: C 286 LYS cc_start: 0.8496 (ptmm) cc_final: 0.8168 (ptmm) REVERT: C 534 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8912 (tptm) REVERT: C 823 GLN cc_start: 0.8799 (mt0) cc_final: 0.8486 (mm-40) REVERT: C 824 GLN cc_start: 0.8570 (pt0) cc_final: 0.8059 (pm20) REVERT: H 40 ARG cc_start: 0.7536 (ttp-170) cc_final: 0.5899 (tpm170) REVERT: I 40 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.5801 (tpm170) REVERT: J 37 ASN cc_start: 0.8457 (m-40) cc_final: 0.8163 (m110) REVERT: J 40 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.5735 (tpm170) outliers start: 32 outliers final: 19 residues processed: 186 average time/residue: 0.6441 time to fit residues: 141.4887 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 : 0.989 ------------------------------------------------------------------------------- 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 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 774 ASN 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 I residue 55 TYR Chi-restraints excluded: chain M residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 271 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 187 optimal weight: 0.4980 chunk 151 optimal weight: 4.9990 chunk 69 optimal weight: 0.0000 chunk 9 optimal weight: 6.9990 chunk 245 optimal weight: 0.0980 chunk 39 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN B 774 ASN B 840 GLN C 774 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.061201 restraints weight = 54250.950| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.24 r_work: 0.2722 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27810 Z= 0.110 Angle : 0.496 7.565 38256 Z= 0.250 Chirality : 0.043 0.263 4803 Planarity : 0.003 0.039 4749 Dihedral : 5.853 59.696 6402 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.46 % Allowed : 9.91 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3513 helix: 2.56 (0.20), residues: 705 sheet: 0.52 (0.17), residues: 930 loop : 0.14 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 322 TYR 0.028 0.001 TYR J 55 PHE 0.030 0.001 PHE B 53 TRP 0.006 0.001 TRP I 49 HIS 0.002 0.000 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00247 (27642) covalent geometry : angle 0.46681 (37797) SS BOND : bond 0.00220 ( 45) SS BOND : angle 1.13540 ( 90) hydrogen bonds : bond 0.03362 ( 1177) hydrogen bonds : angle 4.56976 ( 3279) link_BETA1-4 : bond 0.00452 ( 60) link_BETA1-4 : angle 1.92425 ( 180) link_NAG-ASN : bond 0.00303 ( 63) link_NAG-ASN : angle 1.41718 ( 189) *********************** 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 194 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.176 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: 0.8277 (m-80) cc_final: 0.7882 (m-80) REVERT: A 534 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8845 (tptm) REVERT: A 774 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7307 (t0) REVERT: A 823 GLN cc_start: 0.8798 (mt0) cc_final: 0.8400 (mm-40) REVERT: B 286 LYS cc_start: 0.8505 (ptmm) cc_final: 0.8152 (ptmm) REVERT: B 320 GLU cc_start: 0.8347 (tt0) cc_final: 0.8086 (tt0) REVERT: B 322 ARG cc_start: 0.8804 (mtp85) cc_final: 0.8274 (mtt90) REVERT: B 534 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8930 (tptm) REVERT: B 823 GLN cc_start: 0.8764 (mt0) cc_final: 0.8406 (mm-40) REVERT: B 824 GLN cc_start: 0.8621 (pt0) cc_final: 0.8201 (tt0) REVERT: C 286 LYS cc_start: 0.8514 (ptmm) cc_final: 0.8192 (ptmm) REVERT: C 534 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8887 (tptm) REVERT: C 823 GLN cc_start: 0.8805 (mt0) cc_final: 0.8506 (mm-40) REVERT: C 824 GLN cc_start: 0.8566 (pt0) cc_final: 0.8016 (pm20) REVERT: I 38 TRP cc_start: 0.8168 (m100) cc_final: 0.7640 (m100) REVERT: I 40 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.5807 (tpm170) REVERT: J 37 ASN cc_start: 0.8471 (m-40) cc_final: 0.8161 (m110) REVERT: J 40 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.5704 (ttm170) outliers start: 34 outliers final: 19 residues processed: 186 average time/residue: 0.6345 time to fit residues: 139.3048 Evaluate side-chains 177 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 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 I residue 55 TYR 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 200 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 291 optimal weight: 20.0000 chunk 308 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 840 GLN C 774 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.059460 restraints weight = 54550.037| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.25 r_work: 0.2671 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27810 Z= 0.173 Angle : 0.538 9.355 38256 Z= 0.268 Chirality : 0.044 0.258 4803 Planarity : 0.003 0.043 4749 Dihedral : 6.019 59.527 6402 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.20 % Allowed : 10.51 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.14), residues: 3513 helix: 2.52 (0.20), residues: 705 sheet: 0.49 (0.17), residues: 930 loop : 0.12 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 322 TYR 0.027 0.001 TYR J 55 PHE 0.029 0.001 PHE B 53 TRP 0.007 0.001 TRP I 49 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00405 (27642) covalent geometry : angle 0.50684 (37797) SS BOND : bond 0.00316 ( 45) SS BOND : angle 1.32671 ( 90) hydrogen bonds : bond 0.03810 ( 1177) hydrogen bonds : angle 4.66938 ( 3279) link_BETA1-4 : bond 0.00412 ( 60) link_BETA1-4 : angle 1.97379 ( 180) link_NAG-ASN : bond 0.00329 ( 63) link_NAG-ASN : angle 1.66129 ( 189) *********************** 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 187 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.066 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: 0.8315 (m-80) cc_final: 0.7908 (m-80) REVERT: A 534 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8911 (tptm) REVERT: A 774 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7755 (t0) REVERT: A 823 GLN cc_start: 0.8838 (mt0) cc_final: 0.8520 (mm-40) REVERT: B 286 LYS cc_start: 0.8545 (ptmm) cc_final: 0.8185 (ptmm) REVERT: B 320 GLU cc_start: 0.8335 (tt0) cc_final: 0.8048 (tt0) REVERT: B 322 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8316 (mtt90) REVERT: B 534 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8932 (tptm) REVERT: B 823 GLN cc_start: 0.8806 (mt0) cc_final: 0.8460 (mm-40) REVERT: B 824 GLN cc_start: 0.8629 (pt0) cc_final: 0.8166 (tt0) REVERT: C 286 LYS cc_start: 0.8577 (ptmm) cc_final: 0.8266 (ptmm) REVERT: C 534 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8907 (tptm) REVERT: C 740 MET cc_start: 0.9508 (mtt) cc_final: 0.9284 (mtt) REVERT: C 823 GLN cc_start: 0.8829 (mt0) cc_final: 0.8487 (mm-40) REVERT: H 40 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.5904 (tpm170) REVERT: I 40 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.5862 (tpm170) REVERT: J 37 ASN cc_start: 0.8536 (m-40) cc_final: 0.8248 (m110) REVERT: J 40 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.5765 (tpm170) outliers start: 28 outliers final: 18 residues processed: 181 average time/residue: 0.6174 time to fit residues: 132.1259 Evaluate side-chains 176 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 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 I residue 55 TYR 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 202 optimal weight: 0.4980 chunk 238 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 205 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 158 optimal weight: 0.0030 chunk 226 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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** C 774 ASN C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.061605 restraints weight = 53913.088| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.21 r_work: 0.2714 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2704 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= 0.090 Angle : 0.490 7.107 38256 Z= 0.248 Chirality : 0.043 0.224 4803 Planarity : 0.003 0.039 4749 Dihedral : 5.648 59.828 6402 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.86 % Allowed : 10.60 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3513 helix: 2.60 (0.20), residues: 705 sheet: 0.50 (0.17), residues: 951 loop : 0.14 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 322 TYR 0.026 0.001 TYR J 55 PHE 0.029 0.001 PHE A 53 TRP 0.013 0.001 TRP J 38 HIS 0.002 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00190 (27642) covalent geometry : angle 0.46196 (37797) SS BOND : bond 0.00237 ( 45) SS BOND : angle 1.22571 ( 90) hydrogen bonds : bond 0.03175 ( 1177) hydrogen bonds : angle 4.49383 ( 3279) link_BETA1-4 : bond 0.00468 ( 60) link_BETA1-4 : angle 1.79265 ( 180) link_NAG-ASN : bond 0.00307 ( 63) link_NAG-ASN : angle 1.45482 ( 189) ********************** 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 183 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.062 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: 0.8299 (m-80) cc_final: 0.7939 (m-80) REVERT: A 534 LYS cc_start: 0.9263 (ptpp) cc_final: 0.8865 (tptm) REVERT: A 823 GLN cc_start: 0.8804 (mt0) cc_final: 0.8501 (mm-40) REVERT: B 286 LYS cc_start: 0.8510 (ptmm) cc_final: 0.8178 (ptmt) REVERT: B 320 GLU cc_start: 0.8292 (tt0) cc_final: 0.8027 (tt0) REVERT: B 322 ARG cc_start: 0.8843 (mtp85) cc_final: 0.8379 (mtt90) REVERT: B 534 LYS cc_start: 0.9327 (ptpp) cc_final: 0.8915 (tptm) REVERT: B 823 GLN cc_start: 0.8758 (mt0) cc_final: 0.8415 (mm-40) REVERT: B 824 GLN cc_start: 0.8597 (pt0) cc_final: 0.8118 (tt0) REVERT: C 286 LYS cc_start: 0.8480 (ptmm) cc_final: 0.8164 (ptmt) REVERT: C 534 LYS cc_start: 0.9277 (ptpp) cc_final: 0.8893 (tptm) REVERT: C 740 MET cc_start: 0.9503 (mtt) cc_final: 0.9297 (mtt) REVERT: C 823 GLN cc_start: 0.8803 (mt0) cc_final: 0.8445 (mm-40) REVERT: H 40 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.5985 (tpm170) REVERT: I 38 TRP cc_start: 0.8131 (m100) cc_final: 0.7750 (m100) REVERT: I 40 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.5861 (tpm170) REVERT: J 37 ASN cc_start: 0.8402 (m-40) cc_final: 0.8088 (m110) REVERT: J 40 ARG cc_start: 0.7445 (ttp-170) cc_final: 0.5663 (ttm170) outliers start: 20 outliers final: 15 residues processed: 180 average time/residue: 0.6357 time to fit residues: 135.4479 Evaluate side-chains 168 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 C residue 331 ASN 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 55 TYR 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 50 optimal weight: 0.6980 chunk 319 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 309 optimal weight: 10.0000 chunk 282 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 315 optimal weight: 40.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN C 774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.058558 restraints weight = 54029.767| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.21 r_work: 0.2650 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27810 Z= 0.231 Angle : 0.570 7.332 38256 Z= 0.284 Chirality : 0.046 0.244 4803 Planarity : 0.004 0.056 4749 Dihedral : 6.053 59.409 6390 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.14), residues: 3513 helix: 2.57 (0.20), residues: 696 sheet: 0.53 (0.16), residues: 1026 loop : 0.17 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 322 TYR 0.027 0.001 TYR J 55 PHE 0.029 0.002 PHE B 53 TRP 0.009 0.001 TRP H 38 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00545 (27642) covalent geometry : angle 0.53823 (37797) SS BOND : bond 0.00439 ( 45) SS BOND : angle 1.43095 ( 90) hydrogen bonds : bond 0.04186 ( 1177) hydrogen bonds : angle 4.76871 ( 3279) link_BETA1-4 : bond 0.00428 ( 60) link_BETA1-4 : angle 2.02430 ( 180) link_NAG-ASN : bond 0.00394 ( 63) link_NAG-ASN : angle 1.71451 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7766.50 seconds wall clock time: 133 minutes 19.90 seconds (7999.90 seconds total)