Starting phenix.real_space_refine on Sun Sep 13 02:44:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nqd_0485/09_2026/6nqd_0485.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nqd_0485/09_2026/6nqd_0485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nqd_0485/09_2026/6nqd_0485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nqd_0485/09_2026/6nqd_0485.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nqd_0485/09_2026/6nqd_0485.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nqd_0485/09_2026/6nqd_0485.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nqd_0485/09_2026/6nqd_0485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nqd_0485/09_2026/6nqd_0485.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12645 2.51 5 N 3273 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20175 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "J" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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 chiralities: 3 Chain: "W" 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 chiralities: 4 Chain: "X" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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 chiralities: 3 Chain: "h" 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 chiralities: 4 Chain: "i" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" 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 chiralities: 3 Chain: "s" 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 chiralities: 4 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.34, per 1000 atoms: 0.22 Number of scatterers: 20175 At special positions: 0 Unit cell: (150, 145, 120, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4143 8.00 N 3273 7.00 C 12645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.11 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.11 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.11 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 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 ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN M 8 " - " MAN M 9 " " MAN N 4 " - " MAN N 5 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN X 8 " - " MAN X 9 " " MAN Y 4 " - " MAN Y 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 7 " - " MAN M 10 " " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 7 " - " MAN X 10 " " BMA Y 3 " - " MAN Y 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 10 " " BMA j 3 " - " MAN j 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 8 " " BMA N 3 " - " MAN N 6 " " BMA X 3 " - " MAN X 7 " " MAN X 7 " - " MAN X 8 " " BMA Y 3 " - " MAN Y 6 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA j 3 " - " MAN j 6 " BETA1-4 " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 619 " - " ASN A 160 " " NAG A 620 " - " ASN A 241 " " NAG A 623 " - " ASN A 295 " " NAG A 624 " - " ASN A 301 " " NAG A 627 " - " ASN A 355 " " NAG A 632 " - " ASN A 448 " " NAG B 705 " - " ASN B 611 " " NAG B 706 " - " ASN B 616 " " NAG B 707 " - " ASN B 625 " " NAG C 301 " - " ASN C 82B" " NAG E 619 " - " ASN E 160 " " NAG E 620 " - " ASN E 241 " " NAG E 623 " - " ASN E 295 " " NAG E 624 " - " ASN E 301 " " NAG E 627 " - " ASN E 355 " " NAG E 632 " - " ASN E 448 " " NAG F 705 " - " ASN F 611 " " NAG F 706 " - " ASN F 616 " " NAG F 707 " - " ASN F 625 " " NAG G 301 " - " ASN G 82B" " NAG I 619 " - " ASN I 160 " " NAG I 620 " - " ASN I 241 " " NAG I 623 " - " ASN I 295 " " NAG I 624 " - " ASN I 301 " " NAG I 627 " - " ASN I 355 " " NAG I 632 " - " ASN I 448 " " NAG J 705 " - " ASN J 611 " " NAG J 706 " - " ASN J 616 " " NAG J 707 " - " ASN J 625 " " NAG K 301 " - " ASN K 82B" " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 289 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 386 " " NAG S 1 " - " ASN A 392 " " NAG T 1 " - " ASN A 197 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN B 637 " " NAG X 1 " - " ASN E 234 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 289 " " NAG b 1 " - " ASN E 332 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 392 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 130 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN F 637 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 276 " " NAG k 1 " - " ASN I 156 " " NAG l 1 " - " ASN I 289 " " NAG m 1 " - " ASN I 332 " " NAG n 1 " - " ASN I 386 " " NAG o 1 " - " ASN I 392 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 819.7 milliseconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 45 sheets defined 16.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.043A pdb=" N ASN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 593 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 114 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 476 through 481 removed outlier: 4.043A pdb=" N ASN E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 593 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 660 Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 114 Processing helix chain 'I' and resid 335 through 353 Processing helix chain 'I' and resid 387 through 391 Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.042A pdb=" N ASN I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER J 546 " --> pdb=" O ARG J 542 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 593 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 496 removed outlier: 4.452A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN A 170 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 374 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N LEU A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 312 removed outlier: 6.631A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 59 removed outlier: 5.087A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 496 removed outlier: 4.453A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN E 170 " --> pdb=" O MET E 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS E 374 " --> pdb=" O CYS E 385 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 300 through 312 removed outlier: 6.632A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 393 through 395 Processing sheet with id=AC7, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC9, first strand: chain 'G' and resid 58 through 59 removed outlier: 5.086A pdb=" N TYR G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG G 38 " --> pdb=" O TYR G 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 494 through 496 removed outlier: 4.452A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 46 Processing sheet with id=AD6, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'I' and resid 93 through 94 Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN I 170 " --> pdb=" O MET I 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER I 334 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS I 374 " --> pdb=" O CYS I 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 300 through 312 removed outlier: 6.631A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 393 through 395 Processing sheet with id=AE4, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 5 Processing sheet with id=AE6, first strand: chain 'K' and resid 58 through 59 removed outlier: 5.087A pdb=" N TYR K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG K 38 " --> pdb=" O TYR K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AE8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1782 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: 3.23 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6141 1.35 - 1.48: 5862 1.48 - 1.61: 8430 1.61 - 1.74: 0 1.74 - 1.87: 150 Bond restraints: 20583 Sorted by residual: bond pdb=" C1 NAG o 1 " pdb=" O5 NAG o 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1 NAG J 706 " pdb=" O5 NAG J 706 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C1 NAG F 706 " pdb=" O5 NAG F 706 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 25660 2.38 - 4.76: 2003 4.76 - 7.14: 268 7.14 - 9.52: 56 9.52 - 11.90: 18 Bond angle restraints: 28005 Sorted by residual: angle pdb=" N GLY B 516 " pdb=" CA GLY B 516 " pdb=" C GLY B 516 " ideal model delta sigma weight residual 112.51 124.41 -11.90 1.53e+00 4.27e-01 6.04e+01 angle pdb=" N GLY J 516 " pdb=" CA GLY J 516 " pdb=" C GLY J 516 " ideal model delta sigma weight residual 112.51 124.39 -11.88 1.53e+00 4.27e-01 6.03e+01 angle pdb=" N GLY F 516 " pdb=" CA GLY F 516 " pdb=" C GLY F 516 " ideal model delta sigma weight residual 112.51 124.39 -11.88 1.53e+00 4.27e-01 6.03e+01 angle pdb=" C ALA F 517 " pdb=" N MET F 518 " pdb=" CA MET F 518 " ideal model delta sigma weight residual 122.07 110.71 11.36 1.71e+00 3.42e-01 4.41e+01 angle pdb=" C ALA J 517 " pdb=" N MET J 518 " pdb=" CA MET J 518 " ideal model delta sigma weight residual 122.07 110.72 11.35 1.71e+00 3.42e-01 4.40e+01 ... (remaining 28000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 9920 15.78 - 31.56: 796 31.56 - 47.34: 291 47.34 - 63.12: 69 63.12 - 78.90: 12 Dihedral angle restraints: 11088 sinusoidal: 4221 harmonic: 6867 Sorted by residual: dihedral pdb=" CB CYS I 501 " pdb=" SG CYS I 501 " pdb=" SG CYS J 605 " pdb=" CB CYS J 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.70 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.70 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 11085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 3479 0.177 - 0.354: 106 0.354 - 0.531: 9 0.531 - 0.708: 6 0.708 - 0.885: 3 Chirality restraints: 3603 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN E 289 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG l 1 " pdb=" ND2 ASN I 289 " pdb=" C2 NAG l 1 " pdb=" O5 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 ... (remaining 3600 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 123 " -0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO E 124 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 124 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 124 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 123 " 0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO I 124 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO I 124 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 124 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.056 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO A 124 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.049 5.00e-02 4.00e+02 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3185 2.75 - 3.29: 18917 3.29 - 3.83: 34025 3.83 - 4.36: 37626 4.36 - 4.90: 64547 Nonbonded interactions: 158300 Sorted by model distance: nonbonded pdb=" O ASN E 67 " pdb=" OG1 THR E 71 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 67 " pdb=" OG1 THR A 71 " model vdw 2.213 3.040 nonbonded pdb=" O ASN I 67 " pdb=" OG1 THR I 71 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR E 283 " pdb=" O GLY E 472 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR I 283 " pdb=" O GLY I 472 " model vdw 2.285 3.040 ... (remaining 158295 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'i' } ncs_group { reference = chain 'N' selection = chain 'Y' selection = chain 'j' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'V' selection = chain 'g' selection = chain 'r' } ncs_group { reference = chain 'W' selection = chain 'h' selection = chain 's' } 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: 1.810 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.450 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.012 0.114 20763 Z= 0.552 Angle : 1.531 21.559 28506 Z= 0.766 Chirality : 0.085 0.885 3603 Planarity : 0.008 0.083 3342 Dihedral : 13.921 78.896 6555 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.88 % Favored : 88.35 % Rotamer: Outliers : 8.15 % Allowed : 8.05 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -3.70 (0.15), residues: 2343 helix: -3.03 (0.18), residues: 378 sheet: -1.65 (0.22), residues: 555 loop : -2.74 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG E 298 TYR 0.046 0.005 TYR L 91 PHE 0.043 0.005 PHE A 382 TRP 0.036 0.007 TRP L 35 HIS 0.010 0.002 HIS E 287 Details of bonding type rmsd/Z covalent geometry : bond 0.01216 / 0.55 (20583) covalent geometry : angle 1.40406 / 0.74 (28005) SS BOND : bond 0.02528 / 1.69 ( 39) SS BOND : angle 4.65917 / 3.25 ( 78) hydrogen bonds : bond 0.16482 / 10.94 ( 669) hydrogen bonds : angle 8.65682 / 6.02 ( 1782) link_ALPHA1-2 : bond 0.00507 / 0.34 ( 12) link_ALPHA1-2 : angle 2.33128 / 1.66 ( 36) link_ALPHA1-3 : bond 0.00433 / 0.33 ( 12) link_ALPHA1-3 : angle 2.61612 / 1.92 ( 36) link_ALPHA1-6 : bond 0.00276 / 0.19 ( 9) link_ALPHA1-6 : angle 2.14664 / 1.40 ( 27) link_BETA1-4 : bond 0.00556 / 0.39 ( 45) link_BETA1-4 : angle 2.52544 / 1.79 ( 135) link_NAG-ASN : bond 0.01106 / 0.72 ( 63) link_NAG-ASN : angle 6.70330 / 4.74 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 545 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.7851 (p) cc_final: 0.7587 (t) REVERT: A 169 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7097 (mp10) REVERT: A 207 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8292 (ptpp) REVERT: A 217 TYR cc_start: 0.8851 (m-80) cc_final: 0.8368 (m-10) REVERT: A 218 CYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6364 (m) REVERT: A 362 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6880 (tmtt) REVERT: C 52 TRP cc_start: 0.8814 (t60) cc_final: 0.8530 (t60) REVERT: E 82 GLN cc_start: 0.6928 (pt0) cc_final: 0.6695 (mp10) REVERT: E 207 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8181 (ptpp) REVERT: E 305 THR cc_start: 0.8104 (t) cc_final: 0.7859 (m) REVERT: E 362 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6351 (tmtt) REVERT: H 92 ASP cc_start: 0.7861 (m-30) cc_final: 0.7326 (m-30) REVERT: I 133 SER cc_start: 0.7617 (p) cc_final: 0.7265 (t) REVERT: I 169 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7464 (mp10) REVERT: I 207 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8288 (ptpp) REVERT: I 218 CYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6284 (m) REVERT: I 362 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6999 (tmtt) REVERT: L 24 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7694 (mtp85) outliers start: 160 outliers final: 48 residues processed: 654 average time/residue: 0.1356 time to fit residues: 138.2458 Evaluate side-chains 482 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 426 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 469 ARG Chi-restraints excluded: chain I residue 485 LYS Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 249 HIS A 308 HIS A 354 ASN A 375 HIS B 590 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35AASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 249 HIS E 308 HIS E 354 ASN E 375 HIS F 590 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35AASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 249 HIS I 308 HIS I 354 ASN I 374 HIS I 375 HIS J 590 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35AASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.178165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.153255 restraints weight = 30601.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.156873 restraints weight = 18095.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.159291 restraints weight = 12730.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.160857 restraints weight = 10057.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.161786 restraints weight = 8613.848| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20763 Z= 0.176 Angle : 0.930 13.072 28506 Z= 0.434 Chirality : 0.054 0.507 3603 Planarity : 0.006 0.065 3342 Dihedral : 9.208 59.828 2640 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.13 % Favored : 92.74 % Rotamer: Outliers : 6.12 % Allowed : 14.58 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.78 (0.16), residues: 2343 helix: -1.53 (0.22), residues: 393 sheet: -1.31 (0.22), residues: 558 loop : -2.25 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 304 TYR 0.031 0.002 TYR I 484 PHE 0.029 0.002 PHE E 382 TRP 0.039 0.003 TRP J 628 HIS 0.008 0.001 HIS G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (20583) covalent geometry : angle 0.84699 / 0.42 (28005) SS BOND : bond 0.00598 / 0.37 ( 39) SS BOND : angle 1.85978 / 1.28 ( 78) hydrogen bonds : bond 0.05090 / 3.45 ( 669) hydrogen bonds : angle 7.06541 / 4.87 ( 1782) link_ALPHA1-2 : bond 0.00787 / 0.54 ( 12) link_ALPHA1-2 : angle 1.47178 / 0.98 ( 36) link_ALPHA1-3 : bond 0.00651 / 0.49 ( 12) link_ALPHA1-3 : angle 1.61703 / 1.12 ( 36) link_ALPHA1-6 : bond 0.00258 / 0.17 ( 9) link_ALPHA1-6 : angle 1.70337 / 1.13 ( 27) link_BETA1-4 : bond 0.00525 / 0.36 ( 45) link_BETA1-4 : angle 1.48755 / 1.04 ( 135) link_NAG-ASN : bond 0.00730 / 0.48 ( 63) link_NAG-ASN : angle 4.43740 / 3.22 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 491 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6839 (mp10) REVERT: A 207 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8372 (ptpp) REVERT: A 217 TYR cc_start: 0.8656 (m-80) cc_final: 0.8232 (m-10) REVERT: A 259 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8213 (pp) REVERT: A 305 THR cc_start: 0.8084 (t) cc_final: 0.7719 (m) REVERT: A 377 ASN cc_start: 0.7706 (t0) cc_final: 0.7417 (t0) REVERT: A 484 TYR cc_start: 0.9051 (p90) cc_final: 0.8810 (p90) REVERT: B 603 ILE cc_start: 0.8088 (mm) cc_final: 0.7586 (mt) REVERT: C 52 TRP cc_start: 0.8575 (t60) cc_final: 0.8071 (t60) REVERT: C 54 ARG cc_start: 0.8676 (mpp80) cc_final: 0.8071 (mtm180) REVERT: C 94 THR cc_start: 0.8441 (p) cc_final: 0.8188 (p) REVERT: E 207 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8377 (mttp) REVERT: E 290 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7899 (mt-10) REVERT: E 384 TYR cc_start: 0.6585 (m-10) cc_final: 0.6076 (m-10) REVERT: E 484 TYR cc_start: 0.8867 (p90) cc_final: 0.8592 (p90) REVERT: F 603 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7808 (mt) REVERT: G 73 ASP cc_start: 0.7673 (p0) cc_final: 0.7303 (p0) REVERT: H 47 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (pt) REVERT: H 86 PHE cc_start: 0.6354 (m-10) cc_final: 0.6042 (m-10) REVERT: I 82 GLN cc_start: 0.7673 (mp10) cc_final: 0.7063 (mp10) REVERT: I 207 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8329 (ptpp) REVERT: I 259 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8432 (pp) REVERT: I 298 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8080 (ttp-110) REVERT: I 305 THR cc_start: 0.8219 (t) cc_final: 0.7893 (m) REVERT: I 370 GLU cc_start: 0.8234 (tt0) cc_final: 0.7945 (tt0) REVERT: I 384 TYR cc_start: 0.6839 (m-10) cc_final: 0.6424 (m-10) REVERT: J 603 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7571 (mt) REVERT: J 657 GLU cc_start: 0.7830 (tt0) cc_final: 0.7615 (tt0) REVERT: L 24 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7544 (mtp85) outliers start: 120 outliers final: 62 residues processed: 570 average time/residue: 0.1313 time to fit residues: 118.1166 Evaluate side-chains 515 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 445 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 178 optimal weight: 6.9990 chunk 153 optimal weight: 0.6980 chunk 226 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 0.0670 chunk 122 optimal weight: 0.5980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35AASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35AASN K 43 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.177674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.154584 restraints weight = 30603.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.157386 restraints weight = 17820.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.159094 restraints weight = 12470.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.160304 restraints weight = 9973.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.160782 restraints weight = 9094.926| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20763 Z= 0.152 Angle : 0.868 12.544 28506 Z= 0.399 Chirality : 0.052 0.560 3603 Planarity : 0.005 0.048 3342 Dihedral : 7.654 59.115 2569 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 5.20 % Allowed : 18.30 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.33 (0.17), residues: 2343 helix: -0.75 (0.24), residues: 399 sheet: -0.99 (0.23), residues: 549 loop : -2.10 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 633 TYR 0.027 0.002 TYR B 586 PHE 0.027 0.002 PHE C 30 TRP 0.044 0.003 TRP J 628 HIS 0.004 0.001 HIS E 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (20583) covalent geometry : angle 0.79232 / 0.38 (28005) SS BOND : bond 0.00522 / 0.34 ( 39) SS BOND : angle 1.66959 / 1.12 ( 78) hydrogen bonds : bond 0.04518 / 3.09 ( 669) hydrogen bonds : angle 6.58142 / 4.52 ( 1782) link_ALPHA1-2 : bond 0.00679 / 0.48 ( 12) link_ALPHA1-2 : angle 1.50228 / 1.01 ( 36) link_ALPHA1-3 : bond 0.00690 / 0.50 ( 12) link_ALPHA1-3 : angle 1.48762 / 1.01 ( 36) link_ALPHA1-6 : bond 0.00323 / 0.22 ( 9) link_ALPHA1-6 : angle 1.61250 / 1.07 ( 27) link_BETA1-4 : bond 0.00470 / 0.32 ( 45) link_BETA1-4 : angle 1.39542 / 0.97 ( 135) link_NAG-ASN : bond 0.00579 / 0.38 ( 63) link_NAG-ASN : angle 4.10852 / 2.98 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 485 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7352 (tm-30) cc_final: 0.6795 (mp10) REVERT: A 207 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8333 (ptpp) REVERT: A 259 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8168 (pp) REVERT: A 265 LEU cc_start: 0.8610 (mp) cc_final: 0.8357 (tp) REVERT: A 305 THR cc_start: 0.8064 (t) cc_final: 0.7714 (m) REVERT: A 444 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7379 (ttmt) REVERT: B 603 ILE cc_start: 0.8223 (mm) cc_final: 0.7683 (mt) REVERT: C 54 ARG cc_start: 0.8666 (mpp80) cc_final: 0.8131 (mpp80) REVERT: E 82 GLN cc_start: 0.7483 (pm20) cc_final: 0.7154 (mp10) REVERT: E 169 GLN cc_start: 0.7389 (tm-30) cc_final: 0.6734 (mp10) REVERT: E 207 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8363 (mttp) REVERT: E 217 TYR cc_start: 0.8492 (m-80) cc_final: 0.8235 (m-10) REVERT: E 484 TYR cc_start: 0.8941 (p90) cc_final: 0.8711 (p90) REVERT: F 603 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8041 (mt) REVERT: G 100 LEU cc_start: 0.8983 (mt) cc_final: 0.8754 (mt) REVERT: H 86 PHE cc_start: 0.6477 (m-10) cc_final: 0.6252 (m-10) REVERT: I 82 GLN cc_start: 0.7656 (mp10) cc_final: 0.7445 (mp10) REVERT: I 104 MET cc_start: 0.8988 (tmm) cc_final: 0.8406 (tmm) REVERT: I 181 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8410 (mp) REVERT: I 207 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8208 (ptpp) REVERT: I 298 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7956 (ttp80) REVERT: I 305 THR cc_start: 0.8065 (t) cc_final: 0.7804 (m) REVERT: I 362 LYS cc_start: 0.7299 (tmtt) cc_final: 0.7057 (tttm) REVERT: I 370 GLU cc_start: 0.8187 (tt0) cc_final: 0.7960 (tt0) REVERT: J 603 ILE cc_start: 0.8161 (mm) cc_final: 0.7630 (mt) REVERT: J 657 GLU cc_start: 0.7794 (tt0) cc_final: 0.7564 (tt0) REVERT: J 660 LEU cc_start: 0.6705 (tt) cc_final: 0.6134 (mp) REVERT: L 24 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7585 (mtp85) outliers start: 102 outliers final: 71 residues processed: 544 average time/residue: 0.1325 time to fit residues: 114.2593 Evaluate side-chains 509 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 431 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 161 optimal weight: 0.0270 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35AASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.176298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.152333 restraints weight = 30736.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.155423 restraints weight = 17788.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.157240 restraints weight = 11986.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.157728 restraints weight = 9715.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.158120 restraints weight = 9345.097| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20763 Z= 0.158 Angle : 0.857 12.573 28506 Z= 0.395 Chirality : 0.051 0.406 3603 Planarity : 0.005 0.048 3342 Dihedral : 7.234 59.720 2565 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.37 % Allowed : 19.27 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.11 (0.17), residues: 2343 helix: -0.02 (0.26), residues: 381 sheet: -0.87 (0.23), residues: 531 loop : -2.10 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 46 TYR 0.028 0.002 TYR A 484 PHE 0.028 0.002 PHE D 71 TRP 0.044 0.003 TRP J 628 HIS 0.006 0.001 HIS G 100E Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (20583) covalent geometry : angle 0.78244 / 0.38 (28005) SS BOND : bond 0.00474 / 0.31 ( 39) SS BOND : angle 1.65516 / 1.10 ( 78) hydrogen bonds : bond 0.04444 / 3.03 ( 669) hydrogen bonds : angle 6.24796 / 4.29 ( 1782) link_ALPHA1-2 : bond 0.00598 / 0.41 ( 12) link_ALPHA1-2 : angle 1.52365 / 1.03 ( 36) link_ALPHA1-3 : bond 0.00554 / 0.41 ( 12) link_ALPHA1-3 : angle 1.47278 / 1.00 ( 36) link_ALPHA1-6 : bond 0.00312 / 0.21 ( 9) link_ALPHA1-6 : angle 1.59550 / 1.06 ( 27) link_BETA1-4 : bond 0.00468 / 0.32 ( 45) link_BETA1-4 : angle 1.43795 / 0.99 ( 135) link_NAG-ASN : bond 0.00624 / 0.42 ( 63) link_NAG-ASN : angle 4.03693 / 2.92 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 459 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7387 (tm-30) cc_final: 0.6702 (mp10) REVERT: A 207 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8250 (mttp) REVERT: A 209 SER cc_start: 0.8134 (t) cc_final: 0.7713 (m) REVERT: A 217 TYR cc_start: 0.8416 (m-80) cc_final: 0.8129 (m-80) REVERT: A 259 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8024 (pp) REVERT: A 265 LEU cc_start: 0.8624 (mp) cc_final: 0.8411 (tp) REVERT: A 305 THR cc_start: 0.7997 (t) cc_final: 0.7772 (m) REVERT: A 322 ILE cc_start: 0.5228 (OUTLIER) cc_final: 0.4952 (mp) REVERT: A 456 ARG cc_start: 0.7581 (ptm-80) cc_final: 0.7379 (ptm-80) REVERT: A 484 TYR cc_start: 0.9063 (p90) cc_final: 0.8807 (p90) REVERT: B 603 ILE cc_start: 0.8295 (mm) cc_final: 0.7766 (mt) REVERT: C 32 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8046 (pp) REVERT: C 52 TRP cc_start: 0.8762 (t60) cc_final: 0.8172 (t60) REVERT: C 54 ARG cc_start: 0.8800 (mpp80) cc_final: 0.8064 (mpp80) REVERT: E 82 GLN cc_start: 0.7554 (pm20) cc_final: 0.7324 (mp-120) REVERT: E 207 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8179 (mttp) REVERT: E 217 TYR cc_start: 0.8416 (m-80) cc_final: 0.8131 (m-10) REVERT: E 377 ASN cc_start: 0.7500 (t0) cc_final: 0.7286 (t0) REVERT: E 425 ASN cc_start: 0.7530 (m-40) cc_final: 0.7318 (m-40) REVERT: E 435 TYR cc_start: 0.7708 (t80) cc_final: 0.6925 (t80) REVERT: F 530 MET cc_start: 0.6422 (mmt) cc_final: 0.6042 (mmt) REVERT: F 584 GLU cc_start: 0.8098 (tt0) cc_final: 0.7871 (tt0) REVERT: F 603 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8110 (mt) REVERT: F 628 TRP cc_start: 0.7770 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: H 86 PHE cc_start: 0.6521 (m-10) cc_final: 0.6296 (m-10) REVERT: I 82 GLN cc_start: 0.7679 (mp10) cc_final: 0.7435 (pt0) REVERT: I 161 MET cc_start: 0.8558 (tpp) cc_final: 0.8220 (tpt) REVERT: I 181 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8414 (mp) REVERT: I 207 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8060 (mttp) REVERT: I 209 SER cc_start: 0.8199 (t) cc_final: 0.7730 (m) REVERT: I 305 THR cc_start: 0.8085 (t) cc_final: 0.7837 (m) REVERT: I 362 LYS cc_start: 0.7349 (tmtt) cc_final: 0.7055 (tttm) REVERT: J 603 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7860 (mt) REVERT: J 624 ASN cc_start: 0.8992 (m-40) cc_final: 0.8504 (m-40) REVERT: J 657 GLU cc_start: 0.7822 (tt0) cc_final: 0.7512 (tt0) REVERT: L 37 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7925 (pp30) outliers start: 125 outliers final: 78 residues processed: 536 average time/residue: 0.1301 time to fit residues: 110.7366 Evaluate side-chains 514 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 425 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 186 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.170460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.144354 restraints weight = 31138.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.148274 restraints weight = 19035.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.149987 restraints weight = 12088.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.150712 restraints weight = 9759.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.150948 restraints weight = 9307.322| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20763 Z= 0.208 Angle : 0.888 12.789 28506 Z= 0.411 Chirality : 0.052 0.402 3603 Planarity : 0.005 0.045 3342 Dihedral : 6.896 51.701 2560 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 6.98 % Allowed : 19.83 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.10 (0.17), residues: 2343 helix: -0.18 (0.26), residues: 408 sheet: -1.04 (0.22), residues: 618 loop : -2.02 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 46 TYR 0.037 0.002 TYR E 484 PHE 0.028 0.002 PHE D 71 TRP 0.050 0.003 TRP B 628 HIS 0.006 0.001 HIS G 100E Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (20583) covalent geometry : angle 0.81878 / 0.40 (28005) SS BOND : bond 0.00508 / 0.35 ( 39) SS BOND : angle 1.68243 / 1.12 ( 78) hydrogen bonds : bond 0.04384 / 2.98 ( 669) hydrogen bonds : angle 6.12321 / 4.19 ( 1782) link_ALPHA1-2 : bond 0.00573 / 0.39 ( 12) link_ALPHA1-2 : angle 1.74351 / 1.21 ( 36) link_ALPHA1-3 : bond 0.00510 / 0.38 ( 12) link_ALPHA1-3 : angle 1.53715 / 1.05 ( 36) link_ALPHA1-6 : bond 0.00314 / 0.22 ( 9) link_ALPHA1-6 : angle 1.61889 / 1.08 ( 27) link_BETA1-4 : bond 0.00557 / 0.34 ( 45) link_BETA1-4 : angle 1.35473 / 0.93 ( 135) link_NAG-ASN : bond 0.00716 / 0.47 ( 63) link_NAG-ASN : angle 3.95386 / 2.87 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 447 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8266 (t) cc_final: 0.7721 (m) REVERT: A 217 TYR cc_start: 0.8556 (m-80) cc_final: 0.8289 (m-80) REVERT: A 259 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8110 (pp) REVERT: A 265 LEU cc_start: 0.8641 (mp) cc_final: 0.8406 (tp) REVERT: A 305 THR cc_start: 0.8047 (t) cc_final: 0.7806 (m) REVERT: A 322 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4971 (mp) REVERT: A 483 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8775 (mm) REVERT: B 603 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7884 (mt) REVERT: C 32 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8070 (pp) REVERT: C 54 ARG cc_start: 0.8912 (mpp80) cc_final: 0.8353 (mpp80) REVERT: C 91 PHE cc_start: 0.7491 (m-80) cc_final: 0.7034 (m-80) REVERT: D 45 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8269 (ttp80) REVERT: E 217 TYR cc_start: 0.8514 (m-80) cc_final: 0.8166 (m-10) REVERT: E 377 ASN cc_start: 0.7654 (t0) cc_final: 0.7369 (t0) REVERT: E 435 TYR cc_start: 0.7871 (t80) cc_final: 0.7076 (t80) REVERT: F 591 LYS cc_start: 0.8935 (ptmt) cc_final: 0.8386 (pttt) REVERT: F 603 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8081 (mt) REVERT: F 628 TRP cc_start: 0.8041 (OUTLIER) cc_final: 0.7604 (m-10) REVERT: G 36 TRP cc_start: 0.8152 (m100) cc_final: 0.7088 (m100) REVERT: H 24 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7765 (mtm110) REVERT: I 161 MET cc_start: 0.8578 (tpp) cc_final: 0.8158 (tpt) REVERT: I 181 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8480 (mp) REVERT: I 209 SER cc_start: 0.8131 (t) cc_final: 0.7635 (m) REVERT: I 305 THR cc_start: 0.8091 (t) cc_final: 0.7823 (m) REVERT: I 411 ASN cc_start: 0.6997 (p0) cc_final: 0.6709 (p0) REVERT: I 483 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8943 (mm) REVERT: J 603 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8091 (mt) REVERT: J 624 ASN cc_start: 0.9119 (m-40) cc_final: 0.8632 (m-40) REVERT: J 660 LEU cc_start: 0.6780 (tt) cc_final: 0.6298 (mp) REVERT: K 30 PHE cc_start: 0.8410 (m-80) cc_final: 0.7946 (m-80) REVERT: K 36 TRP cc_start: 0.7827 (m100) cc_final: 0.7453 (m100) REVERT: L 37 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7875 (pp30) outliers start: 137 outliers final: 85 residues processed: 533 average time/residue: 0.1221 time to fit residues: 105.1350 Evaluate side-chains 519 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 423 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 37 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 173 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.166667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.140930 restraints weight = 31045.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.143728 restraints weight = 20822.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.145179 restraints weight = 14485.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.146137 restraints weight = 11826.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.146167 restraints weight = 10801.806| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20763 Z= 0.226 Angle : 0.910 14.872 28506 Z= 0.420 Chirality : 0.053 0.391 3603 Planarity : 0.005 0.061 3342 Dihedral : 6.716 53.133 2547 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.88 % Allowed : 20.29 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.08 (0.17), residues: 2343 helix: -0.42 (0.25), residues: 426 sheet: -1.09 (0.22), residues: 618 loop : -1.89 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 46 TYR 0.032 0.003 TYR A 484 PHE 0.029 0.002 PHE D 71 TRP 0.051 0.003 TRP B 628 HIS 0.005 0.001 HIS E 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (20583) covalent geometry : angle 0.84527 / 0.41 (28005) SS BOND : bond 0.00506 / 0.35 ( 39) SS BOND : angle 1.76376 / 1.18 ( 78) hydrogen bonds : bond 0.04297 / 2.95 ( 669) hydrogen bonds : angle 6.18805 / 4.23 ( 1782) link_ALPHA1-2 : bond 0.00492 / 0.32 ( 12) link_ALPHA1-2 : angle 1.69188 / 1.18 ( 36) link_ALPHA1-3 : bond 0.00543 / 0.41 ( 12) link_ALPHA1-3 : angle 1.57608 / 1.07 ( 36) link_ALPHA1-6 : bond 0.00341 / 0.24 ( 9) link_ALPHA1-6 : angle 1.63241 / 1.08 ( 27) link_BETA1-4 : bond 0.00396 / 0.27 ( 45) link_BETA1-4 : angle 1.32545 / 0.93 ( 135) link_NAG-ASN : bond 0.00633 / 0.42 ( 63) link_NAG-ASN : angle 3.87925 / 2.82 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 460 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8231 (t) cc_final: 0.7714 (m) REVERT: A 259 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8139 (pp) REVERT: A 265 LEU cc_start: 0.8675 (mp) cc_final: 0.8415 (tp) REVERT: A 304 ARG cc_start: 0.8092 (mtm110) cc_final: 0.7813 (mtm110) REVERT: A 322 ILE cc_start: 0.5531 (OUTLIER) cc_final: 0.5194 (mp) REVERT: A 483 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8876 (mm) REVERT: A 484 TYR cc_start: 0.9131 (p90) cc_final: 0.8920 (p90) REVERT: B 603 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8109 (mt) REVERT: C 32 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7565 (pp) REVERT: C 54 ARG cc_start: 0.8876 (mpp80) cc_final: 0.8385 (mpp80) REVERT: D 24 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7476 (mtp85) REVERT: D 45 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8190 (ttp80) REVERT: E 169 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: E 209 SER cc_start: 0.8191 (t) cc_final: 0.7635 (m) REVERT: E 217 TYR cc_start: 0.8600 (m-80) cc_final: 0.8200 (m-10) REVERT: E 376 PHE cc_start: 0.8429 (t80) cc_final: 0.8117 (t80) REVERT: E 377 ASN cc_start: 0.7510 (t0) cc_final: 0.7271 (t0) REVERT: E 411 ASN cc_start: 0.7160 (p0) cc_final: 0.6886 (p0) REVERT: E 435 TYR cc_start: 0.7916 (t80) cc_final: 0.7108 (t80) REVERT: E 484 TYR cc_start: 0.9139 (p90) cc_final: 0.8779 (p90) REVERT: F 577 GLN cc_start: 0.8361 (tp-100) cc_final: 0.8154 (tp-100) REVERT: F 591 LYS cc_start: 0.9035 (ptmt) cc_final: 0.8599 (pttt) REVERT: F 603 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8119 (mt) REVERT: F 628 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.7201 (m-10) REVERT: F 630 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: F 634 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7789 (mm-30) REVERT: G 36 TRP cc_start: 0.8003 (m100) cc_final: 0.7766 (m100) REVERT: H 24 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7817 (mtm110) REVERT: H 32 TRP cc_start: 0.8861 (m100) cc_final: 0.8107 (m100) REVERT: H 89 GLN cc_start: 0.7646 (tt0) cc_final: 0.7320 (tt0) REVERT: I 82 GLN cc_start: 0.7356 (pm20) cc_final: 0.7079 (pt0) REVERT: I 161 MET cc_start: 0.8562 (tpp) cc_final: 0.8015 (tpt) REVERT: I 181 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8667 (mp) REVERT: I 209 SER cc_start: 0.8070 (t) cc_final: 0.7615 (m) REVERT: I 411 ASN cc_start: 0.7220 (p0) cc_final: 0.6937 (p0) REVERT: I 483 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8973 (mm) REVERT: J 616 ASN cc_start: 0.6842 (p0) cc_final: 0.6526 (p0) REVERT: J 624 ASN cc_start: 0.9107 (m-40) cc_final: 0.8594 (m-40) REVERT: K 36 TRP cc_start: 0.7940 (m100) cc_final: 0.7516 (m100) REVERT: L 73 LEU cc_start: 0.7215 (mt) cc_final: 0.7008 (mt) outliers start: 135 outliers final: 93 residues processed: 541 average time/residue: 0.1278 time to fit residues: 111.9378 Evaluate side-chains 544 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 440 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN C 100EHIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.164773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.138379 restraints weight = 31459.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.141247 restraints weight = 21277.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.142794 restraints weight = 14393.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.143795 restraints weight = 12032.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.144512 restraints weight = 10903.057| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20763 Z= 0.228 Angle : 0.899 13.388 28506 Z= 0.418 Chirality : 0.053 0.377 3603 Planarity : 0.005 0.053 3342 Dihedral : 6.692 53.562 2546 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 6.57 % Allowed : 21.46 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.10 (0.17), residues: 2343 helix: -0.25 (0.25), residues: 411 sheet: -1.15 (0.21), residues: 651 loop : -1.94 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 20 TYR 0.026 0.002 TYR A 484 PHE 0.026 0.002 PHE D 71 TRP 0.053 0.003 TRP J 628 HIS 0.005 0.001 HIS E 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (20583) covalent geometry : angle 0.83667 / 0.40 (28005) SS BOND : bond 0.00643 / 0.40 ( 39) SS BOND : angle 1.83452 / 1.24 ( 78) hydrogen bonds : bond 0.04248 / 2.90 ( 669) hydrogen bonds : angle 6.08127 / 4.16 ( 1782) link_ALPHA1-2 : bond 0.00481 / 0.32 ( 12) link_ALPHA1-2 : angle 1.66396 / 1.16 ( 36) link_ALPHA1-3 : bond 0.00531 / 0.41 ( 12) link_ALPHA1-3 : angle 1.55972 / 1.06 ( 36) link_ALPHA1-6 : bond 0.00348 / 0.25 ( 9) link_ALPHA1-6 : angle 1.64712 / 1.09 ( 27) link_BETA1-4 : bond 0.00355 / 0.24 ( 45) link_BETA1-4 : angle 1.29662 / 0.93 ( 135) link_NAG-ASN : bond 0.00598 / 0.39 ( 63) link_NAG-ASN : angle 3.77753 / 2.76 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 461 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: A 209 SER cc_start: 0.8173 (t) cc_final: 0.7645 (m) REVERT: A 259 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8058 (pp) REVERT: A 265 LEU cc_start: 0.8695 (mp) cc_final: 0.8393 (tp) REVERT: A 322 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.5215 (mp) REVERT: A 483 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.8870 (mm) REVERT: C 32 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (pp) REVERT: C 54 ARG cc_start: 0.8839 (mpp80) cc_final: 0.8339 (mpp80) REVERT: C 74 LEU cc_start: 0.8600 (tp) cc_final: 0.8285 (mp) REVERT: D 24 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7509 (mtp85) REVERT: E 169 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: E 181 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8545 (tp) REVERT: E 209 SER cc_start: 0.8141 (t) cc_final: 0.7564 (m) REVERT: E 217 TYR cc_start: 0.8657 (m-80) cc_final: 0.8196 (m-80) REVERT: E 227 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.8207 (ttp80) REVERT: E 395 TRP cc_start: 0.5156 (m-10) cc_final: 0.4778 (m-10) REVERT: E 411 ASN cc_start: 0.7112 (p0) cc_final: 0.6846 (p0) REVERT: E 435 TYR cc_start: 0.7952 (t80) cc_final: 0.7137 (t80) REVERT: E 484 TYR cc_start: 0.9183 (p90) cc_final: 0.8769 (p90) REVERT: F 577 GLN cc_start: 0.8399 (tp-100) cc_final: 0.8166 (tp-100) REVERT: F 591 LYS cc_start: 0.9034 (ptmt) cc_final: 0.8583 (pttt) REVERT: F 630 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7976 (pt0) REVERT: G 32 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7206 (pp) REVERT: H 24 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7810 (mtm110) REVERT: H 32 TRP cc_start: 0.8926 (m100) cc_final: 0.8040 (m100) REVERT: I 82 GLN cc_start: 0.7266 (pm20) cc_final: 0.6944 (mp10) REVERT: I 161 MET cc_start: 0.8550 (tpp) cc_final: 0.8027 (tpt) REVERT: I 181 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8783 (mp) REVERT: I 209 SER cc_start: 0.8051 (t) cc_final: 0.7533 (m) REVERT: I 362 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7038 (tttm) REVERT: I 411 ASN cc_start: 0.7132 (p0) cc_final: 0.6830 (p0) REVERT: I 456 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7287 (ttp80) REVERT: I 483 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9038 (mm) REVERT: I 484 TYR cc_start: 0.9161 (p90) cc_final: 0.8939 (p90) REVERT: J 591 LYS cc_start: 0.8795 (ptmt) cc_final: 0.8453 (ttpt) REVERT: J 616 ASN cc_start: 0.6852 (p0) cc_final: 0.6515 (p0) REVERT: J 624 ASN cc_start: 0.9183 (m-40) cc_final: 0.8684 (m-40) outliers start: 129 outliers final: 94 residues processed: 532 average time/residue: 0.1271 time to fit residues: 108.9019 Evaluate side-chains 544 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 438 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 114 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 375 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 HIS L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.170553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.145197 restraints weight = 31260.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.149667 restraints weight = 19116.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.151447 restraints weight = 11892.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.151981 restraints weight = 9165.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.152378 restraints weight = 9300.635| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 20763 Z= 0.155 Angle : 0.855 13.651 28506 Z= 0.395 Chirality : 0.051 0.362 3603 Planarity : 0.005 0.060 3342 Dihedral : 6.572 50.249 2546 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.71 % Allowed : 22.38 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.17), residues: 2343 helix: -0.04 (0.25), residues: 408 sheet: -1.03 (0.22), residues: 618 loop : -1.86 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 20 TYR 0.023 0.002 TYR A 484 PHE 0.024 0.002 PHE D 71 TRP 0.051 0.003 TRP B 628 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (20583) covalent geometry : angle 0.79336 / 0.38 (28005) SS BOND : bond 0.00510 / 0.38 ( 39) SS BOND : angle 1.93074 / 1.23 ( 78) hydrogen bonds : bond 0.04022 / 2.76 ( 669) hydrogen bonds : angle 5.97145 / 4.09 ( 1782) link_ALPHA1-2 : bond 0.00633 / 0.44 ( 12) link_ALPHA1-2 : angle 1.37493 / 0.94 ( 36) link_ALPHA1-3 : bond 0.00623 / 0.47 ( 12) link_ALPHA1-3 : angle 1.42937 / 0.97 ( 36) link_ALPHA1-6 : bond 0.00339 / 0.23 ( 9) link_ALPHA1-6 : angle 1.61689 / 1.07 ( 27) link_BETA1-4 : bond 0.00417 / 0.28 ( 45) link_BETA1-4 : angle 1.30690 / 0.92 ( 135) link_NAG-ASN : bond 0.00537 / 0.35 ( 63) link_NAG-ASN : angle 3.62586 / 2.64 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 458 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: A 209 SER cc_start: 0.8025 (t) cc_final: 0.7562 (m) REVERT: A 259 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8056 (pp) REVERT: A 265 LEU cc_start: 0.8644 (mp) cc_final: 0.8375 (tp) REVERT: A 322 ILE cc_start: 0.5380 (OUTLIER) cc_final: 0.5084 (mp) REVERT: A 483 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8805 (mm) REVERT: C 52 TRP cc_start: 0.8925 (t60) cc_final: 0.8111 (t60) REVERT: C 54 ARG cc_start: 0.8790 (mpp80) cc_final: 0.7978 (mpp80) REVERT: C 74 LEU cc_start: 0.8499 (tp) cc_final: 0.8186 (mp) REVERT: D 24 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7469 (mtp85) REVERT: E 169 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: E 209 SER cc_start: 0.8013 (t) cc_final: 0.7669 (m) REVERT: E 217 TYR cc_start: 0.8539 (m-80) cc_final: 0.8055 (m-80) REVERT: E 227 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.8140 (ttp80) REVERT: E 411 ASN cc_start: 0.7005 (p0) cc_final: 0.6751 (p0) REVERT: E 435 TYR cc_start: 0.7833 (t80) cc_final: 0.7043 (t80) REVERT: E 484 TYR cc_start: 0.9188 (p90) cc_final: 0.8788 (p90) REVERT: F 577 GLN cc_start: 0.8266 (tp-100) cc_final: 0.8063 (tp-100) REVERT: F 591 LYS cc_start: 0.8954 (ptmt) cc_final: 0.8532 (pttt) REVERT: F 628 TRP cc_start: 0.8246 (OUTLIER) cc_final: 0.7483 (m-10) REVERT: F 630 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: G 36 TRP cc_start: 0.7747 (m100) cc_final: 0.6837 (m100) REVERT: G 54 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8506 (mtm110) REVERT: H 24 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7737 (mtm110) REVERT: H 32 TRP cc_start: 0.8875 (m100) cc_final: 0.8342 (m100) REVERT: I 82 GLN cc_start: 0.7216 (pm20) cc_final: 0.6913 (mp10) REVERT: I 161 MET cc_start: 0.8453 (tpp) cc_final: 0.7920 (tpt) REVERT: I 181 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8598 (mp) REVERT: I 209 SER cc_start: 0.7953 (t) cc_final: 0.7437 (m) REVERT: I 283 THR cc_start: 0.9334 (m) cc_final: 0.9019 (p) REVERT: I 362 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7049 (tttm) REVERT: I 411 ASN cc_start: 0.7059 (p0) cc_final: 0.6772 (p0) REVERT: I 483 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8992 (mm) REVERT: I 484 TYR cc_start: 0.9161 (p90) cc_final: 0.8910 (p90) REVERT: J 591 LYS cc_start: 0.8768 (ptmt) cc_final: 0.8412 (ttpt) REVERT: J 624 ASN cc_start: 0.9132 (m-40) cc_final: 0.8641 (m-40) REVERT: L 35 TRP cc_start: 0.6955 (m-10) cc_final: 0.6720 (m-10) outliers start: 112 outliers final: 89 residues processed: 519 average time/residue: 0.1220 time to fit residues: 102.2150 Evaluate side-chains 525 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 426 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 211 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 375 HIS ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.170655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.145987 restraints weight = 30911.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.148584 restraints weight = 20364.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.150364 restraints weight = 14205.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.151536 restraints weight = 11554.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.151969 restraints weight = 10505.838| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20763 Z= 0.196 Angle : 0.872 13.883 28506 Z= 0.405 Chirality : 0.052 0.367 3603 Planarity : 0.005 0.066 3342 Dihedral : 6.538 50.370 2546 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.35 % Allowed : 23.04 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.18), residues: 2343 helix: -0.05 (0.25), residues: 408 sheet: -1.02 (0.21), residues: 648 loop : -1.87 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 50 TYR 0.022 0.002 TYR A 484 PHE 0.023 0.002 PHE D 71 TRP 0.052 0.003 TRP B 628 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (20583) covalent geometry : angle 0.81127 / 0.39 (28005) SS BOND : bond 0.00590 / 0.36 ( 39) SS BOND : angle 1.76707 / 1.20 ( 78) hydrogen bonds : bond 0.04068 / 2.78 ( 669) hydrogen bonds : angle 5.93327 / 4.05 ( 1782) link_ALPHA1-2 : bond 0.00502 / 0.34 ( 12) link_ALPHA1-2 : angle 1.56930 / 1.08 ( 36) link_ALPHA1-3 : bond 0.00531 / 0.40 ( 12) link_ALPHA1-3 : angle 1.49968 / 1.01 ( 36) link_ALPHA1-6 : bond 0.00332 / 0.22 ( 9) link_ALPHA1-6 : angle 1.61680 / 1.07 ( 27) link_BETA1-4 : bond 0.00385 / 0.26 ( 45) link_BETA1-4 : angle 1.28636 / 0.91 ( 135) link_NAG-ASN : bond 0.00551 / 0.35 ( 63) link_NAG-ASN : angle 3.65623 / 2.67 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 444 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7211 (mp10) REVERT: A 209 SER cc_start: 0.8016 (t) cc_final: 0.7543 (m) REVERT: A 259 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8106 (pp) REVERT: A 265 LEU cc_start: 0.8644 (mp) cc_final: 0.8330 (tp) REVERT: A 322 ILE cc_start: 0.5446 (OUTLIER) cc_final: 0.5132 (mp) REVERT: A 483 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8873 (mm) REVERT: B 591 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8345 (ttpt) REVERT: C 52 TRP cc_start: 0.8978 (t60) cc_final: 0.8566 (t60) REVERT: C 54 ARG cc_start: 0.8817 (mpp80) cc_final: 0.8206 (mpp80) REVERT: C 74 LEU cc_start: 0.8502 (tp) cc_final: 0.8171 (mp) REVERT: D 24 ARG cc_start: 0.7824 (mmt-90) cc_final: 0.7472 (mtp85) REVERT: E 209 SER cc_start: 0.8103 (t) cc_final: 0.7506 (m) REVERT: E 217 TYR cc_start: 0.8578 (m-80) cc_final: 0.8108 (m-80) REVERT: E 227 ARG cc_start: 0.8593 (ttp-170) cc_final: 0.8274 (ttp80) REVERT: E 411 ASN cc_start: 0.7080 (p0) cc_final: 0.6832 (p0) REVERT: E 435 TYR cc_start: 0.7877 (t80) cc_final: 0.7031 (t80) REVERT: E 484 TYR cc_start: 0.9160 (p90) cc_final: 0.8748 (p90) REVERT: F 577 GLN cc_start: 0.8332 (tp-100) cc_final: 0.8101 (tp-100) REVERT: F 591 LYS cc_start: 0.8915 (ptmt) cc_final: 0.8482 (pttt) REVERT: F 630 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: G 36 TRP cc_start: 0.7774 (m100) cc_final: 0.6857 (m100) REVERT: G 52 TRP cc_start: 0.8861 (t60) cc_final: 0.8301 (t60) REVERT: G 54 ARG cc_start: 0.8781 (mtm180) cc_final: 0.8252 (mtm180) REVERT: H 32 TRP cc_start: 0.8837 (m100) cc_final: 0.7907 (m100) REVERT: I 161 MET cc_start: 0.8470 (tpp) cc_final: 0.7944 (tpt) REVERT: I 181 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8689 (mp) REVERT: I 209 SER cc_start: 0.7966 (t) cc_final: 0.7460 (m) REVERT: I 283 THR cc_start: 0.9362 (m) cc_final: 0.9048 (p) REVERT: I 362 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7108 (tttm) REVERT: I 411 ASN cc_start: 0.7084 (p0) cc_final: 0.6795 (p0) REVERT: I 456 ARG cc_start: 0.7313 (ttp80) cc_final: 0.7094 (ttp80) REVERT: I 483 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9021 (mm) REVERT: I 484 TYR cc_start: 0.9145 (p90) cc_final: 0.8905 (p90) REVERT: J 591 LYS cc_start: 0.8763 (ptmt) cc_final: 0.8410 (ttpt) REVERT: J 624 ASN cc_start: 0.9186 (m-40) cc_final: 0.8738 (m-40) outliers start: 105 outliers final: 91 residues processed: 500 average time/residue: 0.1240 time to fit residues: 99.8979 Evaluate side-chains 529 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 430 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 615 SER Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 84 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 189 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 HIS L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.162313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.136588 restraints weight = 31944.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.138799 restraints weight = 22359.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.140665 restraints weight = 15819.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.141606 restraints weight = 11968.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.141885 restraints weight = 11199.469| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 20763 Z= 0.261 Angle : 0.938 14.146 28506 Z= 0.439 Chirality : 0.055 0.384 3603 Planarity : 0.005 0.066 3342 Dihedral : 6.747 53.186 2546 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.25 % Allowed : 23.50 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.10 (0.17), residues: 2343 helix: -0.35 (0.25), residues: 414 sheet: -1.07 (0.21), residues: 642 loop : -1.95 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 304 TYR 0.036 0.003 TYR A 484 PHE 0.020 0.003 PHE L 98 TRP 0.056 0.004 TRP L 35 HIS 0.005 0.001 HIS E 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (20583) covalent geometry : angle 0.87810 / 0.43 (28005) SS BOND : bond 0.00579 / 0.40 ( 39) SS BOND : angle 1.92446 / 1.30 ( 78) hydrogen bonds : bond 0.04269 / 2.91 ( 669) hydrogen bonds : angle 6.07466 / 4.16 ( 1782) link_ALPHA1-2 : bond 0.00497 / 0.33 ( 12) link_ALPHA1-2 : angle 1.79505 / 1.26 ( 36) link_ALPHA1-3 : bond 0.00473 / 0.36 ( 12) link_ALPHA1-3 : angle 1.60804 / 1.09 ( 36) link_ALPHA1-6 : bond 0.00357 / 0.25 ( 9) link_ALPHA1-6 : angle 1.67197 / 1.11 ( 27) link_BETA1-4 : bond 0.00357 / 0.24 ( 45) link_BETA1-4 : angle 1.31312 / 0.95 ( 135) link_NAG-ASN : bond 0.00601 / 0.38 ( 63) link_NAG-ASN : angle 3.78105 / 2.76 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 455 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: A 209 SER cc_start: 0.8105 (t) cc_final: 0.7599 (m) REVERT: A 259 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8177 (pp) REVERT: A 265 LEU cc_start: 0.8610 (mp) cc_final: 0.8283 (tp) REVERT: A 483 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9003 (mm) REVERT: B 584 GLU cc_start: 0.8530 (tt0) cc_final: 0.8312 (tt0) REVERT: C 54 ARG cc_start: 0.8838 (mpp80) cc_final: 0.8567 (mpp80) REVERT: D 24 ARG cc_start: 0.7973 (mmt-90) cc_final: 0.7518 (mtp85) REVERT: E 169 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: E 181 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8558 (tp) REVERT: E 209 SER cc_start: 0.8059 (t) cc_final: 0.7470 (m) REVERT: E 411 ASN cc_start: 0.7079 (p0) cc_final: 0.6793 (p0) REVERT: E 466 GLU cc_start: 0.6783 (tp30) cc_final: 0.6524 (tp30) REVERT: F 577 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8220 (tp-100) REVERT: F 591 LYS cc_start: 0.9019 (ptmt) cc_final: 0.8625 (pttt) REVERT: F 630 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7949 (pt0) REVERT: F 643 TYR cc_start: 0.9283 (m-10) cc_final: 0.8998 (m-10) REVERT: G 36 TRP cc_start: 0.7838 (m100) cc_final: 0.6757 (m100) REVERT: H 32 TRP cc_start: 0.8946 (m100) cc_final: 0.8014 (m100) REVERT: I 161 MET cc_start: 0.8578 (tpp) cc_final: 0.7948 (tpt) REVERT: I 209 SER cc_start: 0.8013 (t) cc_final: 0.7488 (m) REVERT: I 362 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6952 (tttm) REVERT: I 411 ASN cc_start: 0.7142 (p0) cc_final: 0.6826 (p0) REVERT: I 456 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7375 (ttp80) REVERT: I 483 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9086 (mm) REVERT: I 484 TYR cc_start: 0.9186 (p90) cc_final: 0.8930 (p90) REVERT: J 591 LYS cc_start: 0.8920 (ptmt) cc_final: 0.8575 (ttpt) REVERT: J 624 ASN cc_start: 0.9312 (m-40) cc_final: 0.9064 (m-40) REVERT: K 97 THR cc_start: 0.9095 (m) cc_final: 0.8895 (p) outliers start: 103 outliers final: 86 residues processed: 508 average time/residue: 0.1273 time to fit residues: 102.9871 Evaluate side-chains 533 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 439 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 630 GLU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain J residue 658 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 215 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 HIS K 39 GLN ** K 100EHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.168512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.143573 restraints weight = 31550.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.147324 restraints weight = 20666.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.148673 restraints weight = 14132.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.149000 restraints weight = 10605.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.149400 restraints weight = 10900.272| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20763 Z= 0.158 Angle : 0.861 15.015 28506 Z= 0.399 Chirality : 0.051 0.352 3603 Planarity : 0.005 0.067 3342 Dihedral : 6.553 48.755 2546 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.64 % Allowed : 24.26 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.17), residues: 2343 helix: -0.08 (0.25), residues: 408 sheet: -0.99 (0.21), residues: 648 loop : -1.92 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 344 TYR 0.032 0.002 TYR A 484 PHE 0.020 0.002 PHE D 71 TRP 0.052 0.003 TRP B 628 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (20583) covalent geometry : angle 0.80253 / 0.39 (28005) SS BOND : bond 0.00435 / 0.29 ( 39) SS BOND : angle 1.71832 / 1.15 ( 78) hydrogen bonds : bond 0.04011 / 2.75 ( 669) hydrogen bonds : angle 5.90202 / 4.03 ( 1782) link_ALPHA1-2 : bond 0.00617 / 0.43 ( 12) link_ALPHA1-2 : angle 1.33599 / 0.90 ( 36) link_ALPHA1-3 : bond 0.00647 / 0.48 ( 12) link_ALPHA1-3 : angle 1.43173 / 0.96 ( 36) link_ALPHA1-6 : bond 0.00350 / 0.24 ( 9) link_ALPHA1-6 : angle 1.63497 / 1.08 ( 27) link_BETA1-4 : bond 0.00433 / 0.29 ( 45) link_BETA1-4 : angle 1.30750 / 0.93 ( 135) link_NAG-ASN : bond 0.00524 / 0.34 ( 63) link_NAG-ASN : angle 3.57191 / 2.61 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.29 seconds wall clock time: 57 minutes 52.63 seconds (3472.63 seconds total)