Starting phenix.real_space_refine on Thu Mar 5 23:24:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nb6_0403/03_2026/6nb6_0403.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nb6_0403/03_2026/6nb6_0403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nb6_0403/03_2026/6nb6_0403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nb6_0403/03_2026/6nb6_0403.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nb6_0403/03_2026/6nb6_0403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nb6_0403/03_2026/6nb6_0403.map" } resolution = 4.2 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= 0.003 sd= 0.046 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 132 5.16 5 C 16099 2.51 5 N 4307 2.21 5 O 5245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25783 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 7515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 7515 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 998} Chain breaks: 7 Unresolved non-hydrogen bonds: 728 Unresolved non-hydrogen angles: 931 Unresolved non-hydrogen dihedrals: 571 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'ARG:plan': 9, 'ASP:plan': 30, 'GLU:plan': 21, 'GLN:plan1': 8, 'HIS:plan': 4, 'PHE:plan': 16, 'ASN:plan1': 13, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 420 Chain: "B" Number of atoms: 6925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 6925 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 973} Chain breaks: 8 Unresolved non-hydrogen bonds: 1165 Unresolved non-hydrogen angles: 1511 Unresolved non-hydrogen dihedrals: 960 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'ARG:plan': 16, 'TYR:plan': 15, 'HIS:plan': 6, 'ASP:plan': 36, 'GLU:plan': 23, 'PHE:plan': 28, 'ASN:plan1': 24, 'TRP:plan': 4, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 715 Chain: "C" Number of atoms: 7085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 7085 Classifications: {'peptide': 1055} Incomplete info: {'truncation_to_alanine': 335} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1001} Chain breaks: 7 Unresolved non-hydrogen bonds: 1206 Unresolved non-hydrogen angles: 1559 Unresolved non-hydrogen dihedrals: 979 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'ARG:plan': 14, 'PHE:plan': 26, 'TYR:plan': 16, 'GLN:plan1': 12, 'HIS:plan': 6, 'ASP:plan': 43, 'GLU:plan': 22, 'ASN:plan1': 27, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 732 Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 613 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 388 Unresolved non-hydrogen angles: 504 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'ARG:plan': 10, 'PHE:plan': 6, 'ASN:plan1': 4, 'TYR:plan': 7, 'HIS:plan': 3, 'TRP:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 256 Chain: "I" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 618 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 392 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 3, 'ARG:plan': 10, 'PHE:plan': 6, 'ASN:plan1': 4, 'TYR:plan': 7, 'HIS:plan': 3, 'TRP:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 260 Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 557 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 7, 'TYR:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "M" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 552 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 305 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 7, 'TYR:plan': 5, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 189 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" 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: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.41, per 1000 atoms: 0.25 Number of scatterers: 25783 At special positions: 0 Unit cell: (141.11, 149.33, 221.94, 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 132 16.00 O 5245 8.00 N 4307 7.00 C 16099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.14 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.09 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.05 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.05 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.09 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.05 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.06 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.01 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.09 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 93 " 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 ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA p 3 " - " MAN p 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " " BMA b 3 " - " MAN b 5 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 5 " " BMA p 3 " - " MAN p 5 " " BMA r 3 " - " MAN r 5 " 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 G 2 " - " BMA G 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 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 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 X 2 " - " BMA X 3 " " 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 c 2 " - " BMA c 3 " " 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 l 2 " - " BMA l 3 " " 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 p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A1301 " - " ASN A 357 " " NAG A1302 " - " ASN A 65 " " NAG A1303 " - " ASN A 73 " " NAG A1310 " - " ASN A 158 " " NAG A1311 " - " ASN A 227 " " NAG A1315 " - " ASN A 318 " " NAG A1319 " - " ASN A 589 " " NAG B1301 " - " ASN B 357 " " NAG B1302 " - " ASN B 29 " " NAG B1303 " - " ASN B 65 " " NAG B1312 " - " ASN B 227 " " NAG B1322 " - " ASN B 589 " " NAG C1301 " - " ASN C 357 " " NAG C1302 " - " ASN C 29 " " NAG C1303 " - " ASN C 65 " " NAG C1304 " - " ASN C 73 " " NAG C1326 " - " ASN C 589 " " NAG D 1 " - " ASN A 109 " " NAG E 1 " - " ASN A 119 " " NAG F 1 " - " ASN A 269 " " NAG G 1 " - " ASN A 330 " " NAG J 1 " - " ASN A 602 " " NAG K 1 " - " ASN A 691 " " NAG N 1 " - " ASN A 699 " " NAG O 1 " - " ASN A 783 " " NAG P 1 " - " ASN A1056 " " NAG Q 1 " - " ASN A1080 " " NAG R 1 " - " ASN A1116 " " NAG S 1 " - " ASN B 109 " " NAG T 1 " - " ASN B 119 " " NAG U 1 " - " ASN B 158 " " NAG V 1 " - " ASN B 269 " " NAG W 1 " - " ASN B 318 " " NAG X 1 " - " ASN B 330 " " NAG Y 1 " - " ASN B 602 " " NAG Z 1 " - " ASN B 691 " " NAG a 1 " - " ASN B 699 " " NAG b 1 " - " ASN B 783 " " NAG c 1 " - " ASN B1056 " " NAG d 1 " - " ASN B1080 " " NAG e 1 " - " ASN B1116 " " NAG f 1 " - " ASN C 109 " " NAG g 1 " - " ASN C 119 " " NAG h 1 " - " ASN C 158 " " NAG i 1 " - " ASN C 227 " " NAG j 1 " - " ASN C 269 " " NAG k 1 " - " ASN C 318 " " NAG l 1 " - " ASN C 330 " " NAG m 1 " - " ASN C 602 " " NAG n 1 " - " ASN C 691 " " NAG o 1 " - " ASN C 699 " " NAG p 1 " - " ASN C 783 " " NAG q 1 " - " ASN C1056 " " NAG r 1 " - " ASN C1080 " " NAG s 1 " - " ASN C1116 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6732 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 62 sheets defined 23.1% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.671A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.006A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.746A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.958A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.047A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 967 through 1015 Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 370 through 377 removed outlier: 4.933A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.252A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.524A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.641A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 763 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 867 through 870 removed outlier: 3.846A pdb=" N PHE B 870 " --> pdb=" O GLY B 867 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 867 through 870' Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.008A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 959 through 964 Processing helix chain 'B' and resid 967 through 1015 Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.612A pdb=" N PHE C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 370 through 377 removed outlier: 3.827A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 3.950A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 725 removed outlier: 4.045A pdb=" N ILE C 724 " --> pdb=" O CYS C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 Processing helix chain 'C' and resid 798 through 806 Processing helix chain 'C' and resid 848 through 867 removed outlier: 3.570A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.222A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 959 through 964 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.052A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 108 through 112 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 108 through 112 Processing helix chain 'L' and resid 84 through 88 Processing helix chain 'M' and resid 84 through 88 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 8.407A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N HIS A 181 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE A 203 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG A 183 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLN A 201 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N PHE A 185 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY A 199 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHE A 187 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR A 197 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ASN A 189 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR A 195 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.702A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 59 removed outlier: 7.526A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.536A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 131 through 138 removed outlier: 6.867A pdb=" N GLU A 131 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 152 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ASN A 135 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 10.623A pdb=" N THR A 150 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 616 removed outlier: 5.305A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 635 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 631 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 5.998A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.551A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB3, first strand: chain 'A' and resid 640 through 646 removed outlier: 5.715A pdb=" N THR A 678 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A 644 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 683 through 684 removed outlier: 5.966A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 697 Processing sheet with id=AB6, first strand: chain 'A' and resid 700 through 710 removed outlier: 3.587A pdb=" N ALA A1038 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.317A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB9, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AC1, first strand: chain 'A' and resid 821 through 823 Processing sheet with id=AC2, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.664A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 31 through 34 removed outlier: 7.550A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N PHE B 213 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG B 38 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU B 216 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 31 through 34 Processing sheet with id=AC5, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.716A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 51 through 59 removed outlier: 7.612A pdb=" N THR B 261 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP B 277 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET B 263 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA B 275 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 265 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 80 through 82 removed outlier: 6.203A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 615 through 616 removed outlier: 5.291A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 341 through 345 removed outlier: 6.281A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 341 through 345 removed outlier: 6.997A pdb=" N GLU B 502 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 382 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER B 500 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 384 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL B 498 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 386 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 496 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL B 388 " --> pdb=" O TYR B 494 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR B 494 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 501 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N MET B 417 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY B 418 " --> pdb=" O TYR B 367 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AD3, first strand: chain 'B' and resid 640 through 646 removed outlier: 5.058A pdb=" N THR B 678 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR B 644 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.941A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 700 through 710 removed outlier: 3.540A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.396A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AD8, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.863A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 31 through 34 removed outlier: 7.768A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 51 through 59 removed outlier: 7.509A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 81 through 82 removed outlier: 13.451A pdb=" N PHE C 231 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N ASP C 134 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N ALA C 233 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU C 235 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 152 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'C' and resid 615 through 616 removed outlier: 5.294A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 303 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.653A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS C 419 " --> pdb=" O LEU C 499 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.047A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE8, first strand: chain 'C' and resid 640 through 646 removed outlier: 5.185A pdb=" N THR C 678 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR C 644 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 693 through 697 Processing sheet with id=AF1, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.629A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.305A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF4, first strand: chain 'C' and resid 821 through 822 Processing sheet with id=AF5, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.582A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.695A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.002A pdb=" N GLN L 42 " --> pdb=" O ARG L 51 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG L 51 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 14 Processing sheet with id=AG6, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.090A pdb=" N GLN M 42 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ARG M 51 " --> pdb=" O GLN M 42 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 10 through 12 1260 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7089 1.33 - 1.46: 7552 1.46 - 1.59: 11437 1.59 - 1.73: 1 1.73 - 1.86: 168 Bond restraints: 26247 Sorted by residual: bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.559 -0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" C1 NAG k 2 " pdb=" O5 NAG k 2 " ideal model delta sigma weight residual 1.406 1.558 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.553 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C1 NAG j 2 " pdb=" O5 NAG j 2 " ideal model delta sigma weight residual 1.406 1.551 -0.145 2.00e-02 2.50e+03 5.28e+01 ... (remaining 26242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.51: 35591 5.51 - 11.03: 401 11.03 - 16.54: 2 16.54 - 22.05: 3 22.05 - 27.57: 2 Bond angle restraints: 35999 Sorted by residual: angle pdb=" N LEU B 927 " pdb=" CA LEU B 927 " pdb=" CB LEU B 927 " ideal model delta sigma weight residual 111.43 91.02 20.41 1.48e+00 4.57e-01 1.90e+02 angle pdb=" N ALA C 926 " pdb=" CA ALA C 926 " pdb=" C ALA C 926 " ideal model delta sigma weight residual 110.80 138.37 -27.57 2.13e+00 2.20e-01 1.68e+02 angle pdb=" N ALA B 926 " pdb=" CA ALA B 926 " pdb=" C ALA B 926 " ideal model delta sigma weight residual 110.80 138.18 -27.38 2.13e+00 2.20e-01 1.65e+02 angle pdb=" N LEU C 927 " pdb=" CA LEU C 927 " pdb=" CB LEU C 927 " ideal model delta sigma weight residual 111.43 92.53 18.90 1.48e+00 4.57e-01 1.63e+02 angle pdb=" CG1 VAL B 808 " pdb=" CB VAL B 808 " pdb=" CG2 VAL B 808 " ideal model delta sigma weight residual 110.80 131.78 -20.98 2.20e+00 2.07e-01 9.10e+01 ... (remaining 35994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 16471 21.83 - 43.65: 537 43.65 - 65.48: 122 65.48 - 87.31: 208 87.31 - 109.13: 149 Dihedral angle restraints: 17487 sinusoidal: 7075 harmonic: 10412 Sorted by residual: dihedral pdb=" C ALA C 926 " pdb=" N ALA C 926 " pdb=" CA ALA C 926 " pdb=" CB ALA C 926 " ideal model delta harmonic sigma weight residual -122.60 -160.02 37.42 0 2.50e+00 1.60e-01 2.24e+02 dihedral pdb=" N ALA C 926 " pdb=" C ALA C 926 " pdb=" CA ALA C 926 " pdb=" CB ALA C 926 " ideal model delta harmonic sigma weight residual 122.90 160.30 -37.40 0 2.50e+00 1.60e-01 2.24e+02 dihedral pdb=" N ALA B 926 " pdb=" C ALA B 926 " pdb=" CA ALA B 926 " pdb=" CB ALA B 926 " ideal model delta harmonic sigma weight residual 122.90 158.18 -35.28 0 2.50e+00 1.60e-01 1.99e+02 ... (remaining 17484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 4678 0.356 - 0.713: 48 0.713 - 1.069: 0 1.069 - 1.426: 0 1.426 - 1.782: 2 Chirality restraints: 4728 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.32e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.19e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-02 2.50e+03 2.18e+02 ... (remaining 4725 not shown) Planarity restraints: 4624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 269 " 0.065 2.00e-02 2.50e+03 6.61e-02 5.46e+01 pdb=" CG ASN B 269 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 269 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 269 " -0.098 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 269 " 0.057 2.00e-02 2.50e+03 5.95e-02 4.42e+01 pdb=" CG ASN A 269 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 269 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 269 " -0.090 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 65 " 0.033 2.00e-02 2.50e+03 3.37e-02 1.42e+01 pdb=" CG ASN A 65 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 65 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 65 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.041 2.00e-02 2.50e+03 ... (remaining 4621 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7113 2.79 - 3.32: 22433 3.32 - 3.85: 39920 3.85 - 4.37: 43173 4.37 - 4.90: 74127 Nonbonded interactions: 186766 Sorted by model distance: nonbonded pdb=" O PHE C1071 " pdb=" OG1 THR C1102 " model vdw 2.264 3.040 nonbonded pdb=" NZ LYS A 793 " pdb=" OG1 THR A 795 " model vdw 2.285 3.120 nonbonded pdb=" O PHE B1071 " pdb=" OG1 THR B1102 " model vdw 2.291 3.040 nonbonded pdb=" O PHE A1071 " pdb=" OG1 THR A1102 " model vdw 2.296 3.040 nonbonded pdb=" N ASN A 109 " pdb=" OD1 ASN A 109 " model vdw 2.351 3.120 ... (remaining 186761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 31 or (resid 32 through 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 39 or (resid 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 through 54 or (res \ id 55 through 58 and (name N or name CA or name C or name O or name CB )) or res \ id 59 through 65 or (resid 66 through 67 and (name N or name CA or name C or nam \ e O or name CB )) or resid 68 or (resid 69 through 78 and (name N or name CA or \ name C or name O or name CB )) or resid 79 through 100 or (resid 101 through 103 \ and (name N or name CA or name C or name O or name CB )) or resid 104 through 1 \ 37 or resid 149 through 160 or (resid 161 through 168 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 197 or (resid 198 and (name \ N or name CA or name C or name O or name CB )) or resid 199 through 237 or resid \ 250 through 260 or (resid 261 and (name N or name CA or name C or name O or nam \ e CB )) or resid 262 through 271 or (resid 272 through 277 and (name N or name C \ A or name C or name O or name CB )) or resid 278 through 295 or (resid 296 and ( \ name N or name CA or name C or name O or name CB )) or resid 297 through 300 or \ (resid 301 and (name N or name CA or name C or name O or name CB )) or resid 302 \ through 306 or (resid 307 through 308 and (name N or name CA or name C or name \ O or name CB )) or resid 309 through 324 or (resid 325 and (name N or name CA or \ name C or name O or name CB )) or (resid 326 through 329 and (name N or name CA \ or name C or name O or name CB )) or resid 330 through 331 or (resid 332 throug \ h 334 and (name N or name CA or name C or name O or name CB )) or resid 335 thro \ ugh 336 or (resid 337 through 347 and (name N or name CA or name C or name O or \ name CB )) or resid 348 or (resid 349 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 or (resid 358 through 365 and (name N or \ name CA or name C or name O or name CB )) or resid 366 or (resid 367 and (name \ N or name CA or name C or name O or name CB )) or resid 368 or (resid 369 throug \ h 377 and (name N or name CA or name C or name O or name CB )) or resid 378 or ( \ resid 379 through 390 and (name N or name CA or name C or name O or name CB )) o \ r (resid 391 through 398 and (name N or name CA or name C or name O or name CB ) \ ) or resid 399 through 404 or (resid 405 through 412 and (name N or name CA or n \ ame C or name O or name CB )) or resid 413 through 415 or (resid 416 through 417 \ and (name N or name CA or name C or name O or name CB )) or resid 418 through 4 \ 19 or (resid 420 through 433 and (name N or name CA or name C or name O or name \ CB )) or resid 434 or (resid 435 through 445 and (name N or name CA or name C or \ name O or name CB )) or (resid 446 through 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 or (resid 451 through 458 and (name N or n \ ame CA or name C or name O or name CB )) or resid 459 or (resid 460 through 461 \ and (name N or name CA or name C or name O or name CB )) or resid 462 through 47 \ 2 or (resid 473 and (name N or name CA or name C or name O or name CB )) or resi \ d 474 or (resid 475 through 476 and (name N or name CA or name C or name O or na \ me CB )) or resid 477 through 478 or (resid 479 through 481 and (name N or name \ CA or name C or name O or name CB )) or resid 482 or (resid 483 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 492 and (name N or name CA or \ name C or name O or name CB )) or resid 493 or (resid 494 through 502 and (name \ N or name CA or name C or name O or name CB )) or (resid 509 through 510 and (n \ ame N or name CA or name C or name O or name CB )) or resid 511 through 513 or ( \ resid 514 through 520 and (name N or name CA or name C or name O or name CB )) o \ r resid 521 or (resid 522 and (name N or name CA or name C or name O or name CB \ )) or resid 523 through 548 or (resid 549 through 550 and (name N or name CA or \ name C or name O or name CB )) or resid 551 through 559 or (resid 560 and (name \ N or name CA or name C or name O or name CB )) or resid 561 through 565 or (resi \ d 566 and (name N or name CA or name C or name O or name CB )) or resid 567 thro \ ugh 592 or (resid 593 and (name N or name CA or name C or name O or name CB )) o \ r resid 594 through 604 or (resid 605 and (name N or name CA or name C or name O \ or name CB )) or resid 606 through 610 or (resid 611 through 612 and (name N or \ name CA or name C or name O or name CB )) or resid 613 through 625 or (resid 62 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 627 through \ 661 or (resid 662 through 671 and (name N or name CA or name C or name O or name \ CB )) or resid 672 through 683 or (resid 684 and (name N or name CA or name C o \ r name O or name CB )) or resid 685 through 740 or (resid 741 and (name N or nam \ e CA or name C or name O or name CB )) or resid 742 through 756 or (resid 757 an \ d (name N or name CA or name C or name O or name CB )) or resid 758 through 761 \ or (resid 762 and (name N or name CA or name C or name O or name CB )) or resid \ 763 through 767 or (resid 768 and (name N or name CA or name C or name O or name \ CB )) or resid 769 through 808 or resid 836 through 837 or (resid 838 and (name \ N or name CA or name C or name O or name CB )) or resid 839 through 848 or (res \ id 849 and (name N or name CA or name C or name O or name CB )) or resid 850 thr \ ough 899 or (resid 900 and (name N or name CA or name C or name O or name CB )) \ or resid 901 through 902 or (resid 903 and (name N or name CA or name C or name \ O or name CB )) or resid 904 through 931 or (resid 932 and (name N or name CA or \ name C or name O or name CB )) or resid 933 through 971 or (resid 972 and (name \ N or name CA or name C or name O or name CB )) or resid 973 through 975 or (res \ id 976 and (name N or name CA or name C or name O or name CB )) or resid 977 thr \ ough 1012 or (resid 1013 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1014 through 1022 or (resid 1023 and (name N or name CA or name C or \ name O or name CB )) or resid 1024 through 1072 or (resid 1073 through 1074 and \ (name N or name CA or name C or name O or name CB )) or resid 1075 through 1099 \ or (resid 1100 and (name N or name CA or name C or name O or name CB )) or resid \ 1101 through 1108 or (resid 1109 and (name N or name CA or name C or name O or \ name CB )) or resid 1110 through 1116 or (resid 1117 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1118 through 1311)) selection = (chain 'B' and (resid 18 through 21 or (resid 31 through 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 48 or (res \ id 49 through 52 and (name N or name CA or name C or name O or name CB )) or res \ id 53 through 54 or (resid 55 through 58 and (name N or name CA or name C or nam \ e O or name CB )) or resid 59 through 63 or (resid 64 and (name N or name CA or \ name C or name O or name CB )) or resid 65 through 137 or resid 149 through 168 \ or resid 180 through 199 or (resid 200 through 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 212 or (resid 213 through 217 a \ nd (name N or name CA or name C or name O or name CB )) or resid 218 through 259 \ or (resid 260 through 261 and (name N or name CA or name C or name O or name CB \ )) or resid 262 or (resid 263 and (name N or name CA or name C or name O or nam \ e CB )) or resid 264 or (resid 265 and (name N or name CA or name C or name O or \ name CB )) or resid 266 through 284 or (resid 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 through 295 or (resid 296 and (name N o \ r name CA or name C or name O or name CB )) or resid 297 through 300 or (resid 3 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 302 through \ 306 or (resid 307 through 308 and (name N or name CA or name C or name O or nam \ e CB )) or resid 309 through 437 or (resid 438 through 445 and (name N or name C \ A or name C or name O or name CB )) or resid 446 through 515 or (resid 516 throu \ gh 520 and (name N or name CA or name C or name O or name CB )) or resid 521 or \ (resid 522 and (name N or name CA or name C or name O or name CB )) or resid 523 \ through 548 or (resid 549 through 550 and (name N or name CA or name C or name \ O or name CB )) or resid 551 through 553 or (resid 554 and (name N or name CA or \ name C or name O or name CB )) or resid 555 through 559 or (resid 560 and (name \ N or name CA or name C or name O or name CB )) or resid 561 through 565 or (res \ id 566 and (name N or name CA or name C or name O or name CB )) or resid 567 thr \ ough 598 or (resid 599 through 600 and (name N or name CA or name C or name O or \ name CB )) or resid 601 through 604 or (resid 605 and (name N or name CA or nam \ e C or name O or name CB )) or resid 606 through 610 or (resid 611 through 612 a \ nd (name N or name CA or name C or name O or name CB )) or resid 613 through 625 \ or (resid 626 and (name N or name CA or name C or name O or name CB )) or resid \ 627 through 639 or (resid 640 and (name N or name CA or name C or name O or nam \ e CB )) or resid 641 through 642 or (resid 643 and (name N or name CA or name C \ or name O or name CB )) or resid 644 through 661 or (resid 662 through 671 and ( \ name N or name CA or name C or name O or name CB )) or resid 672 through 740 or \ (resid 741 and (name N or name CA or name C or name O or name CB )) or resid 742 \ through 756 or (resid 757 and (name N or name CA or name C or name O or name CB \ )) or resid 758 through 767 or (resid 768 and (name N or name CA or name C or n \ ame O or name CB )) or resid 769 through 808 or (resid 836 and (name N or name C \ A or name C or name O or name CB )) or resid 837 or (resid 838 and (name N or na \ me CA or name C or name O or name CB )) or resid 839 through 848 or (resid 849 a \ nd (name N or name CA or name C or name O or name CB )) or resid 850 through 899 \ or (resid 900 and (name N or name CA or name C or name O or name CB )) or resid \ 901 through 902 or (resid 903 and (name N or name CA or name C or name O or nam \ e CB )) or resid 904 through 931 or (resid 932 and (name N or name CA or name C \ or name O or name CB )) or resid 933 through 966 or (resid 967 and (name N or na \ me CA or name C or name O or name CB )) or resid 968 through 975 or (resid 976 a \ nd (name N or name CA or name C or name O or name CB )) or resid 977 through 101 \ 2 or (resid 1013 and (name N or name CA or name C or name O or name CB )) or res \ id 1014 through 1116 or (resid 1117 and (name N or name CA or name C or name O o \ r name CB )) or resid 1118 through 1122 or (resid 1123 through 1124 and (name N \ or name CA or name C or name O or name CB )) or resid 1125 through 1322)) selection = (chain 'C' and (resid 18 through 21 or resid 31 through 37 or (resid 38 and (nam \ e N or name CA or name C or name O or name CB )) or resid 39 or (resid 40 and (n \ ame N or name CA or name C or name O or name CB )) or resid 41 through 51 or (re \ sid 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 55 or (resid 56 through 58 and (name N or name CA or name C or name O or nam \ e CB )) or resid 59 or (resid 60 and (name N or name CA or name C or name O or n \ ame CB )) or resid 61 through 66 or (resid 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 or (resid 69 through 78 and (name N or name C \ A or name C or name O or name CB )) or resid 79 through 82 or (resid 83 through \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 100 or (resid 101 through 103 and (name N or name CA or name C or name O or name \ CB )) or resid 104 through 137 or resid 149 through 160 or (resid 161 through 1 \ 91 and (name N or name CA or name C or name O or name CB )) or resid 192 through \ 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or r \ esid 197 through 208 or (resid 209 and (name N or name CA or name C or name O or \ name CB )) or resid 210 through 212 or (resid 213 through 217 and (name N or na \ me CA or name C or name O or name CB )) or resid 218 through 219 or (resid 220 t \ hrough 222 and (name N or name CA or name C or name O or name CB )) or resid 223 \ through 237 or resid 250 through 260 or (resid 261 and (name N or name CA or na \ me C or name O or name CB )) or resid 262 or (resid 263 and (name N or name CA o \ r name C or name O or name CB )) or resid 264 through 270 or (resid 271 through \ 277 and (name N or name CA or name C or name O or name CB )) or resid 278 throug \ h 284 or (resid 285 and (name N or name CA or name C or name O or name CB )) or \ resid 286 through 337 or (resid 338 through 347 and (name N or name CA or name C \ or name O or name CB )) or resid 348 through 409 or (resid 410 through 412 and \ (name N or name CA or name C or name O or name CB )) or resid 413 through 474 or \ (resid 475 through 476 and (name N or name CA or name C or name O or name CB )) \ or resid 477 through 483 or resid 492 through 502 or resid 509 through 518 or ( \ resid 519 through 520 and (name N or name CA or name C or name O or name CB )) o \ r resid 521 through 568 or (resid 569 and (name N or name CA or name C or name O \ or name CB )) or resid 570 through 592 or (resid 593 and (name N or name CA or \ name C or name O or name CB )) or resid 594 through 598 or (resid 599 through 60 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 601 through \ 663 or resid 671 through 706 or (resid 707 and (name N or name CA or name C or n \ ame O or name CB )) or resid 708 through 808 or resid 836 through 917 or (resid \ 918 and (name N or name CA or name C or name O or name CB )) or resid 919 throug \ h 971 or (resid 972 and (name N or name CA or name C or name O or name CB )) or \ resid 973 through 1022 or (resid 1023 and (name N or name CA or name C or name O \ or name CB )) or resid 1024 through 1072 or (resid 1073 through 1074 and (name \ N or name CA or name C or name O or name CB )) or resid 1075 through 1099 or (re \ sid 1100 and (name N or name CA or name C or name O or name CB )) or resid 1101 \ through 1108 or (resid 1109 and (name N or name CA or name C or name O or name C \ B )) or resid 1110 through 1122 or (resid 1123 through 1124 and (name N or name \ CA or name C or name O or name CB )) or resid 1125 through 1326)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'N' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 's' } ncs_group { reference = chain 'H' selection = (chain 'I' and resid 2 through 124) } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'b' selection = chain 'e' selection = chain 'p' selection = chain 'r' } ncs_group { reference = (chain 'L' and resid 3 through 111) selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.360 Find NCS groups from input model: 0.950 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.017 0.153 26444 Z= 0.898 Angle : 1.537 27.568 36542 Z= 0.927 Chirality : 0.105 1.782 4728 Planarity : 0.006 0.029 4569 Dihedral : 19.893 109.135 10611 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.33 % Favored : 96.44 % Rotamer: Outliers : 0.42 % Allowed : 1.90 % Favored : 97.68 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 6.67 % 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: 0.22 (0.14), residues: 3541 helix: 0.45 (0.18), residues: 702 sheet: 0.81 (0.17), residues: 849 loop : -0.19 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1089 TYR 0.037 0.005 TYR C 677 PHE 0.024 0.004 PHE A 629 TRP 0.028 0.005 TRP C1084 HIS 0.007 0.001 HIS B 661 Details of bonding type rmsd covalent geometry : bond 0.01657 (26247) covalent geometry : angle 1.49946 (35999) SS BOND : bond 0.02411 ( 48) SS BOND : angle 4.09066 ( 96) hydrogen bonds : bond 0.18201 ( 1206) hydrogen bonds : angle 8.03083 ( 3345) link_ALPHA1-3 : bond 0.03968 ( 9) link_ALPHA1-3 : angle 1.39936 ( 27) link_ALPHA1-6 : bond 0.02246 ( 10) link_ALPHA1-6 : angle 2.44236 ( 30) link_BETA1-4 : bond 0.03520 ( 75) link_BETA1-4 : angle 3.08107 ( 225) link_NAG-ASN : bond 0.03619 ( 55) link_NAG-ASN : angle 2.89721 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 310 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 LEU cc_start: 0.9093 (tp) cc_final: 0.8806 (mt) REVERT: A 868 TRP cc_start: 0.5301 (m100) cc_final: 0.4295 (m100) REVERT: B 263 MET cc_start: 0.8442 (ttp) cc_final: 0.7672 (tpp) REVERT: B 285 GLU cc_start: 0.9038 (tt0) cc_final: 0.8611 (tt0) REVERT: B 302 THR cc_start: 0.8805 (p) cc_final: 0.8532 (p) REVERT: B 894 THR cc_start: 0.8070 (m) cc_final: 0.7609 (p) REVERT: C 263 MET cc_start: 0.8590 (ttp) cc_final: 0.8340 (ttp) REVERT: C 679 MET cc_start: 0.8644 (ptm) cc_final: 0.8410 (ptm) REVERT: C 759 ASN cc_start: 0.9046 (m-40) cc_final: 0.8652 (m-40) REVERT: C 770 MET cc_start: 0.7697 (mmm) cc_final: 0.7336 (mmm) outliers start: 8 outliers final: 6 residues processed: 318 average time/residue: 0.1626 time to fit residues: 82.7624 Evaluate side-chains 148 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0770 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 GLN A 661 HIS A 733 ASN A 786 GLN A 984 GLN A1095 GLN B 661 HIS B 786 GLN B1101 ASN C 661 HIS C1095 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.086110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.063443 restraints weight = 117476.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064967 restraints weight = 67852.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065957 restraints weight = 47233.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066599 restraints weight = 37452.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066874 restraints weight = 32311.071| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26444 Z= 0.160 Angle : 0.842 20.895 36542 Z= 0.380 Chirality : 0.055 0.794 4728 Planarity : 0.005 0.066 4569 Dihedral : 13.684 81.686 6766 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.21 % Allowed : 1.58 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3541 helix: 1.73 (0.20), residues: 702 sheet: 0.81 (0.17), residues: 832 loop : -0.14 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C1001 TYR 0.020 0.001 TYR A1049 PHE 0.019 0.001 PHE A 329 TRP 0.009 0.001 TRP C1084 HIS 0.006 0.001 HIS B 661 Details of bonding type rmsd covalent geometry : bond 0.00324 (26247) covalent geometry : angle 0.73944 (35999) SS BOND : bond 0.00339 ( 48) SS BOND : angle 1.73241 ( 96) hydrogen bonds : bond 0.05912 ( 1206) hydrogen bonds : angle 5.95938 ( 3345) link_ALPHA1-3 : bond 0.01149 ( 9) link_ALPHA1-3 : angle 2.68103 ( 27) link_ALPHA1-6 : bond 0.01007 ( 10) link_ALPHA1-6 : angle 1.83860 ( 30) link_BETA1-4 : bond 0.00788 ( 75) link_BETA1-4 : angle 3.84305 ( 225) link_NAG-ASN : bond 0.00676 ( 55) link_NAG-ASN : angle 3.75779 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ILE cc_start: 0.9128 (mp) cc_final: 0.8767 (mm) REVERT: A 622 TYR cc_start: 0.7723 (t80) cc_final: 0.7303 (t80) REVERT: A 722 MET cc_start: 0.9353 (tpp) cc_final: 0.8933 (tpt) REVERT: A 730 GLU cc_start: 0.8858 (mp0) cc_final: 0.8469 (pm20) REVERT: B 263 MET cc_start: 0.8484 (ttp) cc_final: 0.7640 (tpp) REVERT: B 302 THR cc_start: 0.9034 (p) cc_final: 0.8699 (p) REVERT: B 528 ASN cc_start: 0.8695 (t0) cc_final: 0.8273 (m-40) REVERT: B 722 MET cc_start: 0.8429 (tpt) cc_final: 0.8020 (tpp) REVERT: B 804 LEU cc_start: 0.9486 (mp) cc_final: 0.9143 (mt) REVERT: B 894 THR cc_start: 0.8136 (m) cc_final: 0.7652 (p) REVERT: C 558 PHE cc_start: 0.8673 (m-80) cc_final: 0.8388 (m-80) REVERT: C 679 MET cc_start: 0.8700 (ptm) cc_final: 0.8198 (ptm) REVERT: C 770 MET cc_start: 0.8032 (mmm) cc_final: 0.7474 (mmm) REVERT: C 851 MET cc_start: 0.8850 (mtp) cc_final: 0.8397 (mtp) outliers start: 4 outliers final: 1 residues processed: 208 average time/residue: 0.1438 time to fit residues: 50.7746 Evaluate side-chains 122 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 41 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 140 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 222 optimal weight: 2.9990 chunk 314 optimal weight: 30.0000 chunk 66 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 786 GLN C1030 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.085594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062767 restraints weight = 118405.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065004 restraints weight = 70342.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065536 restraints weight = 43898.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065967 restraints weight = 33766.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066178 restraints weight = 31480.872| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26444 Z= 0.138 Angle : 0.727 17.862 36542 Z= 0.331 Chirality : 0.051 0.555 4728 Planarity : 0.004 0.061 4569 Dihedral : 9.627 71.771 6766 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3541 helix: 2.09 (0.20), residues: 698 sheet: 0.72 (0.17), residues: 878 loop : -0.17 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1001 TYR 0.014 0.001 TYR A1049 PHE 0.017 0.001 PHE A 364 TRP 0.017 0.001 TRP A 868 HIS 0.003 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00276 (26247) covalent geometry : angle 0.64517 (35999) SS BOND : bond 0.00238 ( 48) SS BOND : angle 1.78202 ( 96) hydrogen bonds : bond 0.04845 ( 1206) hydrogen bonds : angle 5.29238 ( 3345) link_ALPHA1-3 : bond 0.01402 ( 9) link_ALPHA1-3 : angle 1.89180 ( 27) link_ALPHA1-6 : bond 0.01580 ( 10) link_ALPHA1-6 : angle 1.80567 ( 30) link_BETA1-4 : bond 0.00653 ( 75) link_BETA1-4 : angle 3.28980 ( 225) link_NAG-ASN : bond 0.00562 ( 55) link_NAG-ASN : angle 2.90971 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.7972 (m-80) cc_final: 0.7643 (m-80) REVERT: A 622 TYR cc_start: 0.7607 (t80) cc_final: 0.7085 (t80) REVERT: A 730 GLU cc_start: 0.8850 (mp0) cc_final: 0.8534 (pm20) REVERT: A 884 MET cc_start: 0.9479 (tpp) cc_final: 0.9272 (tpp) REVERT: B 263 MET cc_start: 0.8334 (ttp) cc_final: 0.7643 (tpp) REVERT: B 285 GLU cc_start: 0.8896 (tt0) cc_final: 0.8692 (tt0) REVERT: B 722 MET cc_start: 0.8267 (tpt) cc_final: 0.7982 (tpp) REVERT: B 894 THR cc_start: 0.8079 (m) cc_final: 0.7650 (p) REVERT: B 1011 MET cc_start: 0.8984 (tmm) cc_final: 0.8428 (ttp) REVERT: C 558 PHE cc_start: 0.8608 (m-80) cc_final: 0.8259 (m-80) REVERT: C 679 MET cc_start: 0.8743 (ptm) cc_final: 0.8330 (ptm) REVERT: C 709 MET cc_start: 0.8924 (mtp) cc_final: 0.8426 (ptp) REVERT: C 770 MET cc_start: 0.7988 (mmm) cc_final: 0.7462 (mmm) REVERT: C 851 MET cc_start: 0.8907 (mtp) cc_final: 0.8575 (mtp) REVERT: C 972 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9058 (tp30) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1463 time to fit residues: 45.2958 Evaluate side-chains 117 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 20.0000 chunk 182 optimal weight: 0.6980 chunk 265 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 285 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 316 optimal weight: 0.9980 chunk 332 optimal weight: 40.0000 chunk 331 optimal weight: 20.0000 chunk 199 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 GLN B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.085022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061971 restraints weight = 119014.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.063475 restraints weight = 68045.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064493 restraints weight = 47240.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065139 restraints weight = 37270.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065465 restraints weight = 32254.845| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26444 Z= 0.142 Angle : 0.717 16.189 36542 Z= 0.323 Chirality : 0.050 0.520 4728 Planarity : 0.004 0.070 4569 Dihedral : 8.529 66.172 6766 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3541 helix: 2.14 (0.20), residues: 700 sheet: 0.71 (0.16), residues: 903 loop : -0.17 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 758 TYR 0.022 0.001 TYR A 886 PHE 0.019 0.001 PHE A 888 TRP 0.013 0.001 TRP A 868 HIS 0.006 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00301 (26247) covalent geometry : angle 0.62804 (35999) SS BOND : bond 0.00261 ( 48) SS BOND : angle 1.96915 ( 96) hydrogen bonds : bond 0.04525 ( 1206) hydrogen bonds : angle 5.09346 ( 3345) link_ALPHA1-3 : bond 0.01354 ( 9) link_ALPHA1-3 : angle 2.48943 ( 27) link_ALPHA1-6 : bond 0.01668 ( 10) link_ALPHA1-6 : angle 1.94460 ( 30) link_BETA1-4 : bond 0.00575 ( 75) link_BETA1-4 : angle 3.11003 ( 225) link_NAG-ASN : bond 0.00449 ( 55) link_NAG-ASN : angle 3.25767 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8061 (m-80) cc_final: 0.7859 (m-80) REVERT: A 622 TYR cc_start: 0.7722 (t80) cc_final: 0.7114 (t80) REVERT: A 730 GLU cc_start: 0.8931 (mp0) cc_final: 0.8566 (pm20) REVERT: B 263 MET cc_start: 0.8322 (ttp) cc_final: 0.7742 (tpp) REVERT: B 709 MET cc_start: 0.7921 (ptp) cc_final: 0.7419 (ptt) REVERT: B 722 MET cc_start: 0.8312 (tpt) cc_final: 0.8107 (tpp) REVERT: B 894 THR cc_start: 0.8245 (m) cc_final: 0.7750 (p) REVERT: B 1011 MET cc_start: 0.9040 (tmm) cc_final: 0.8458 (ttp) REVERT: C 558 PHE cc_start: 0.8751 (m-80) cc_final: 0.8257 (m-80) REVERT: C 679 MET cc_start: 0.8787 (ptm) cc_final: 0.8424 (ptm) REVERT: C 713 MET cc_start: 0.8511 (ptp) cc_final: 0.8268 (ptm) REVERT: C 770 MET cc_start: 0.7880 (mmm) cc_final: 0.7443 (mmm) REVERT: C 851 MET cc_start: 0.8968 (mtp) cc_final: 0.8555 (mtp) REVERT: C 972 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8806 (mm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1483 time to fit residues: 42.4554 Evaluate side-chains 109 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 242 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 278 optimal weight: 0.0270 chunk 30 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.083954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061423 restraints weight = 118341.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063146 restraints weight = 74513.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063609 restraints weight = 53913.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.064173 restraints weight = 40644.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064255 restraints weight = 35291.521| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26444 Z= 0.147 Angle : 0.689 15.324 36542 Z= 0.313 Chirality : 0.049 0.507 4728 Planarity : 0.004 0.064 4569 Dihedral : 8.020 63.083 6766 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.05 % Allowed : 1.69 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3541 helix: 2.11 (0.20), residues: 698 sheet: 0.76 (0.17), residues: 878 loop : -0.21 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 758 TYR 0.017 0.001 TYR B1049 PHE 0.015 0.001 PHE A 629 TRP 0.017 0.002 TRP A 868 HIS 0.008 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00317 (26247) covalent geometry : angle 0.61608 (35999) SS BOND : bond 0.00233 ( 48) SS BOND : angle 1.76806 ( 96) hydrogen bonds : bond 0.04444 ( 1206) hydrogen bonds : angle 4.99010 ( 3345) link_ALPHA1-3 : bond 0.01380 ( 9) link_ALPHA1-3 : angle 2.25132 ( 27) link_ALPHA1-6 : bond 0.01747 ( 10) link_ALPHA1-6 : angle 2.02722 ( 30) link_BETA1-4 : bond 0.00582 ( 75) link_BETA1-4 : angle 2.95571 ( 225) link_NAG-ASN : bond 0.00442 ( 55) link_NAG-ASN : angle 2.67017 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 622 TYR cc_start: 0.7760 (t80) cc_final: 0.7084 (t80) REVERT: A 730 GLU cc_start: 0.8998 (mp0) cc_final: 0.8609 (pm20) REVERT: B 285 GLU cc_start: 0.9227 (tt0) cc_final: 0.8939 (tt0) REVERT: B 722 MET cc_start: 0.8402 (tpt) cc_final: 0.8154 (tpp) REVERT: B 894 THR cc_start: 0.8341 (m) cc_final: 0.7851 (p) REVERT: B 1011 MET cc_start: 0.9126 (tmm) cc_final: 0.8901 (tmm) REVERT: C 558 PHE cc_start: 0.8728 (m-80) cc_final: 0.8238 (m-80) REVERT: C 679 MET cc_start: 0.8761 (ptm) cc_final: 0.8428 (ptm) REVERT: C 709 MET cc_start: 0.8862 (mtp) cc_final: 0.8538 (ptp) REVERT: C 755 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7476 (tm-30) REVERT: C 770 MET cc_start: 0.7907 (mmm) cc_final: 0.7501 (mmm) REVERT: C 851 MET cc_start: 0.8968 (mtp) cc_final: 0.8547 (mtp) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1491 time to fit residues: 39.2017 Evaluate side-chains 107 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 296 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 175 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 312 optimal weight: 50.0000 chunk 190 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN A1030 HIS B1030 HIS C 786 GLN C 896 ASN C 917 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.081537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058826 restraints weight = 119745.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060612 restraints weight = 73823.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060911 restraints weight = 45331.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061270 restraints weight = 39755.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061254 restraints weight = 36226.623| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26444 Z= 0.194 Angle : 0.750 16.120 36542 Z= 0.347 Chirality : 0.050 0.500 4728 Planarity : 0.004 0.066 4569 Dihedral : 7.956 61.449 6766 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3541 helix: 1.67 (0.20), residues: 696 sheet: 0.63 (0.17), residues: 890 loop : -0.26 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 797 TYR 0.033 0.002 TYR A 886 PHE 0.022 0.002 PHE A 629 TRP 0.028 0.002 TRP C 868 HIS 0.010 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00427 (26247) covalent geometry : angle 0.67918 (35999) SS BOND : bond 0.00485 ( 48) SS BOND : angle 2.01496 ( 96) hydrogen bonds : bond 0.04872 ( 1206) hydrogen bonds : angle 5.09822 ( 3345) link_ALPHA1-3 : bond 0.01361 ( 9) link_ALPHA1-3 : angle 2.25297 ( 27) link_ALPHA1-6 : bond 0.01813 ( 10) link_ALPHA1-6 : angle 2.07431 ( 30) link_BETA1-4 : bond 0.00591 ( 75) link_BETA1-4 : angle 2.90905 ( 225) link_NAG-ASN : bond 0.00476 ( 55) link_NAG-ASN : angle 2.92536 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 999 GLU cc_start: 0.8348 (tp30) cc_final: 0.8016 (tm-30) REVERT: B 263 MET cc_start: 0.8301 (ttm) cc_final: 0.7960 (tpp) REVERT: B 560 ASP cc_start: 0.8591 (t0) cc_final: 0.8384 (t70) REVERT: B 689 TYR cc_start: 0.7730 (t80) cc_final: 0.7465 (t80) REVERT: C 558 PHE cc_start: 0.8774 (m-80) cc_final: 0.8203 (m-80) REVERT: C 679 MET cc_start: 0.8740 (ptm) cc_final: 0.8393 (ptm) REVERT: C 722 MET cc_start: 0.8568 (tpp) cc_final: 0.8242 (tpt) REVERT: C 770 MET cc_start: 0.8067 (mmm) cc_final: 0.7780 (mmm) REVERT: C 851 MET cc_start: 0.9042 (mtp) cc_final: 0.8587 (mtp) REVERT: C 972 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8838 (mm-30) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1365 time to fit residues: 33.0274 Evaluate side-chains 101 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 67 optimal weight: 0.5980 chunk 135 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 286 optimal weight: 0.5980 chunk 283 optimal weight: 0.0270 chunk 336 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1018 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.060245 restraints weight = 119180.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061882 restraints weight = 71980.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.062554 restraints weight = 51495.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.063153 restraints weight = 38613.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063419 restraints weight = 34503.296| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26444 Z= 0.130 Angle : 0.687 15.215 36542 Z= 0.311 Chirality : 0.049 0.488 4728 Planarity : 0.004 0.068 4569 Dihedral : 7.595 59.066 6766 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3541 helix: 1.96 (0.20), residues: 701 sheet: 0.76 (0.17), residues: 864 loop : -0.22 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1001 TYR 0.019 0.001 TYR A 886 PHE 0.022 0.001 PHE A 888 TRP 0.028 0.002 TRP C 868 HIS 0.003 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00274 (26247) covalent geometry : angle 0.61046 (35999) SS BOND : bond 0.00279 ( 48) SS BOND : angle 1.93094 ( 96) hydrogen bonds : bond 0.04307 ( 1206) hydrogen bonds : angle 4.82800 ( 3345) link_ALPHA1-3 : bond 0.01334 ( 9) link_ALPHA1-3 : angle 2.23821 ( 27) link_ALPHA1-6 : bond 0.01863 ( 10) link_ALPHA1-6 : angle 2.14222 ( 30) link_BETA1-4 : bond 0.00604 ( 75) link_BETA1-4 : angle 2.77028 ( 225) link_NAG-ASN : bond 0.00431 ( 55) link_NAG-ASN : angle 2.97972 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 999 GLU cc_start: 0.8366 (tp30) cc_final: 0.8054 (tm-30) REVERT: B 263 MET cc_start: 0.8238 (ttm) cc_final: 0.7984 (tpp) REVERT: B 545 PHE cc_start: 0.7843 (m-10) cc_final: 0.7596 (m-80) REVERT: B 689 TYR cc_start: 0.7753 (t80) cc_final: 0.7447 (t80) REVERT: B 713 MET cc_start: 0.8441 (ppp) cc_final: 0.7274 (ppp) REVERT: B 722 MET cc_start: 0.8287 (tpt) cc_final: 0.7969 (tpt) REVERT: C 558 PHE cc_start: 0.8683 (m-80) cc_final: 0.8144 (m-80) REVERT: C 713 MET cc_start: 0.8581 (ptp) cc_final: 0.8332 (ptm) REVERT: C 851 MET cc_start: 0.9056 (mtp) cc_final: 0.8626 (mtp) REVERT: C 972 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8750 (mm-30) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1339 time to fit residues: 34.4456 Evaluate side-chains 99 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 158 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN C1018 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.060301 restraints weight = 118974.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.062414 restraints weight = 73112.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062799 restraints weight = 49356.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063277 restraints weight = 38181.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063368 restraints weight = 33397.821| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26444 Z= 0.136 Angle : 0.679 14.816 36542 Z= 0.307 Chirality : 0.049 0.477 4728 Planarity : 0.004 0.089 4569 Dihedral : 7.385 57.797 6766 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3541 helix: 1.81 (0.20), residues: 719 sheet: 0.72 (0.17), residues: 876 loop : -0.21 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1001 TYR 0.025 0.001 TYR C 855 PHE 0.015 0.001 PHE C 545 TRP 0.029 0.001 TRP C 868 HIS 0.005 0.001 HIS C1040 Details of bonding type rmsd covalent geometry : bond 0.00289 (26247) covalent geometry : angle 0.60988 (35999) SS BOND : bond 0.00246 ( 48) SS BOND : angle 1.81120 ( 96) hydrogen bonds : bond 0.04184 ( 1206) hydrogen bonds : angle 4.74108 ( 3345) link_ALPHA1-3 : bond 0.01358 ( 9) link_ALPHA1-3 : angle 2.25290 ( 27) link_ALPHA1-6 : bond 0.01845 ( 10) link_ALPHA1-6 : angle 2.12343 ( 30) link_BETA1-4 : bond 0.00596 ( 75) link_BETA1-4 : angle 2.70841 ( 225) link_NAG-ASN : bond 0.00415 ( 55) link_NAG-ASN : angle 2.74050 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 999 GLU cc_start: 0.8382 (tp30) cc_final: 0.8110 (tm-30) REVERT: B 263 MET cc_start: 0.8291 (ttm) cc_final: 0.7931 (tpp) REVERT: B 713 MET cc_start: 0.8537 (ppp) cc_final: 0.7555 (ppp) REVERT: B 722 MET cc_start: 0.8344 (tpt) cc_final: 0.8003 (tpt) REVERT: C 558 PHE cc_start: 0.8691 (m-80) cc_final: 0.8175 (m-80) REVERT: C 851 MET cc_start: 0.8998 (mtp) cc_final: 0.8567 (mtp) REVERT: C 972 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8692 (mm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1443 time to fit residues: 34.0507 Evaluate side-chains 97 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 211 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 168 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 269 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059304 restraints weight = 120004.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061009 restraints weight = 76338.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061184 restraints weight = 49092.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061545 restraints weight = 42543.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061586 restraints weight = 40012.164| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26444 Z= 0.167 Angle : 0.698 14.407 36542 Z= 0.321 Chirality : 0.049 0.474 4728 Planarity : 0.004 0.073 4569 Dihedral : 7.396 57.497 6766 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3541 helix: 1.67 (0.20), residues: 720 sheet: 0.68 (0.17), residues: 917 loop : -0.25 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 620 TYR 0.028 0.001 TYR A 886 PHE 0.018 0.001 PHE A 888 TRP 0.017 0.002 TRP C 619 HIS 0.006 0.002 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00366 (26247) covalent geometry : angle 0.63324 (35999) SS BOND : bond 0.00300 ( 48) SS BOND : angle 1.85861 ( 96) hydrogen bonds : bond 0.04433 ( 1206) hydrogen bonds : angle 4.83039 ( 3345) link_ALPHA1-3 : bond 0.01259 ( 9) link_ALPHA1-3 : angle 2.11235 ( 27) link_ALPHA1-6 : bond 0.01895 ( 10) link_ALPHA1-6 : angle 2.10944 ( 30) link_BETA1-4 : bond 0.00599 ( 75) link_BETA1-4 : angle 2.69529 ( 225) link_NAG-ASN : bond 0.00402 ( 55) link_NAG-ASN : angle 2.65695 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 263 MET cc_start: 0.8262 (ttm) cc_final: 0.7884 (tpp) REVERT: B 560 ASP cc_start: 0.8717 (t0) cc_final: 0.8470 (t70) REVERT: B 713 MET cc_start: 0.8691 (ppp) cc_final: 0.7798 (ppp) REVERT: B 722 MET cc_start: 0.8379 (tpt) cc_final: 0.8041 (tpt) REVERT: C 558 PHE cc_start: 0.8738 (m-80) cc_final: 0.8179 (m-80) REVERT: C 851 MET cc_start: 0.8965 (mtp) cc_final: 0.8579 (mtp) REVERT: C 972 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8707 (mm-30) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1408 time to fit residues: 32.0049 Evaluate side-chains 97 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 254 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 160 optimal weight: 0.0030 chunk 188 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 238 optimal weight: 0.0170 chunk 133 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 343 optimal weight: 40.0000 overall best weight: 0.8032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059579 restraints weight = 120383.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.061339 restraints weight = 76636.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.061689 restraints weight = 53992.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062106 restraints weight = 42039.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062184 restraints weight = 37173.222| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26444 Z= 0.131 Angle : 0.669 14.330 36542 Z= 0.304 Chirality : 0.048 0.464 4728 Planarity : 0.004 0.075 4569 Dihedral : 7.190 55.958 6766 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3541 helix: 1.82 (0.20), residues: 714 sheet: 0.71 (0.17), residues: 901 loop : -0.18 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 620 TYR 0.017 0.001 TYR B1049 PHE 0.017 0.001 PHE A 888 TRP 0.012 0.001 TRP C 868 HIS 0.004 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00279 (26247) covalent geometry : angle 0.60441 (35999) SS BOND : bond 0.00294 ( 48) SS BOND : angle 1.98199 ( 96) hydrogen bonds : bond 0.04106 ( 1206) hydrogen bonds : angle 4.70068 ( 3345) link_ALPHA1-3 : bond 0.01273 ( 9) link_ALPHA1-3 : angle 2.13550 ( 27) link_ALPHA1-6 : bond 0.01898 ( 10) link_ALPHA1-6 : angle 2.13581 ( 30) link_BETA1-4 : bond 0.00601 ( 75) link_BETA1-4 : angle 2.61887 ( 225) link_NAG-ASN : bond 0.00398 ( 55) link_NAG-ASN : angle 2.50148 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7082 Ramachandran restraints generated. 3541 Oldfield, 0 Emsley, 3541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 263 MET cc_start: 0.8225 (ttm) cc_final: 0.7878 (tpp) REVERT: B 560 ASP cc_start: 0.8726 (t0) cc_final: 0.8486 (t70) REVERT: B 713 MET cc_start: 0.8675 (ppp) cc_final: 0.7788 (ppp) REVERT: B 722 MET cc_start: 0.8347 (tpt) cc_final: 0.8001 (tpt) REVERT: B 755 GLU cc_start: 0.8525 (tp30) cc_final: 0.8250 (tm-30) REVERT: C 558 PHE cc_start: 0.8669 (m-80) cc_final: 0.8131 (m-80) REVERT: C 851 MET cc_start: 0.9010 (mtp) cc_final: 0.8655 (mtp) REVERT: C 972 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8598 (mm-30) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1387 time to fit residues: 32.1456 Evaluate side-chains 98 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 50 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 293 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 331 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 347 ASN A 641 HIS A 786 GLN A 917 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.079150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.056646 restraints weight = 121375.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.058402 restraints weight = 77555.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058428 restraints weight = 49716.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058782 restraints weight = 44592.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.058790 restraints weight = 41305.436| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 26444 Z= 0.272 Angle : 0.824 14.338 36542 Z= 0.389 Chirality : 0.051 0.469 4728 Planarity : 0.005 0.100 4569 Dihedral : 7.916 58.677 6766 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3541 helix: 1.17 (0.19), residues: 705 sheet: 0.60 (0.17), residues: 865 loop : -0.41 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1001 TYR 0.024 0.002 TYR C 886 PHE 0.025 0.002 PHE A 629 TRP 0.039 0.003 TRP C 868 HIS 0.011 0.002 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00604 (26247) covalent geometry : angle 0.76296 (35999) SS BOND : bond 0.00414 ( 48) SS BOND : angle 2.20979 ( 96) hydrogen bonds : bond 0.05407 ( 1206) hydrogen bonds : angle 5.35194 ( 3345) link_ALPHA1-3 : bond 0.01295 ( 9) link_ALPHA1-3 : angle 1.96183 ( 27) link_ALPHA1-6 : bond 0.01888 ( 10) link_ALPHA1-6 : angle 2.10409 ( 30) link_BETA1-4 : bond 0.00639 ( 75) link_BETA1-4 : angle 2.79717 ( 225) link_NAG-ASN : bond 0.00531 ( 55) link_NAG-ASN : angle 2.93357 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.43 seconds wall clock time: 61 minutes 0.17 seconds (3660.17 seconds total)