Starting phenix.real_space_refine on Sat Mar 7 10:52:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z0v_11024/03_2026/6z0v_11024.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z0v_11024/03_2026/6z0v_11024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6z0v_11024/03_2026/6z0v_11024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z0v_11024/03_2026/6z0v_11024.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z0v_11024/03_2026/6z0v_11024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z0v_11024/03_2026/6z0v_11024.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 360 5.16 5 C 26664 2.51 5 N 7224 2.21 5 O 8712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42972 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "C" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "E" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "G" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "I" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "K" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "M" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "O" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "Q" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "S" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "V" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "X" Number of atoms: 3502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 452, 3473 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 3514 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "O" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "Q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "V" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "X" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1004 SG CYS A 134 14.386 109.609 27.844 1.00 65.97 S ATOM 1056 SG CYS A 141 14.243 105.715 28.023 1.00 58.88 S ATOM 4506 SG CYS C 134 19.597 66.394 27.887 1.00 63.68 S ATOM 4558 SG CYS C 141 21.377 62.905 28.014 1.00 55.04 S ATOM 8008 SG CYS E 134 45.561 31.521 27.853 1.00 64.63 S ATOM 8060 SG CYS E 141 48.873 29.500 28.030 1.00 57.45 S ATOM 11510 SG CYS G 134 85.563 14.386 27.844 1.00 66.05 S ATOM 11562 SG CYS G 141 89.457 14.243 28.023 1.00 58.70 S ATOM 15012 SG CYS I 134 128.780 19.599 27.883 1.00 64.08 S ATOM 15064 SG CYS I 141 132.265 21.377 28.012 1.00 54.99 S ATOM 18514 SG CYS K 134 163.651 45.559 27.852 1.00 64.64 S ATOM 18566 SG CYS K 141 165.673 48.874 28.030 1.00 57.35 S ATOM 22016 SG CYS M 134 180.786 85.563 27.845 1.00 66.09 S ATOM 22068 SG CYS M 141 180.929 89.458 28.023 1.00 58.75 S ATOM 25518 SG CYS O 134 175.572 128.780 27.885 1.00 63.94 S ATOM 25570 SG CYS O 141 173.795 132.267 28.014 1.00 54.96 S ATOM 29020 SG CYS Q 134 149.613 163.646 27.853 1.00 64.93 S ATOM 29072 SG CYS Q 141 146.300 165.673 28.030 1.00 56.85 S ATOM 32522 SG CYS S 134 109.609 180.786 27.845 1.00 65.98 S ATOM 32574 SG CYS S 141 105.715 180.929 28.023 1.00 58.80 S ATOM 36024 SG CYS V 134 66.393 175.573 27.888 1.00 63.74 S ATOM 36076 SG CYS V 141 62.906 173.797 28.014 1.00 54.73 S ATOM 39526 SG CYS X 134 31.528 149.594 27.854 1.00 64.62 S ATOM 39578 SG CYS X 141 29.498 146.299 28.030 1.00 57.13 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N ACYS G 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.50 residue: pdb=" N ACYS I 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.50 residue: pdb=" N ACYS K 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.50 residue: pdb=" N ACYS M 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS M 236 " occ=0.50 residue: pdb=" N ACYS O 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS O 236 " occ=0.50 residue: pdb=" N ACYS Q 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS Q 236 " occ=0.50 residue: pdb=" N ACYS S 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS S 236 " occ=0.50 residue: pdb=" N ACYS V 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS V 236 " occ=0.50 residue: pdb=" N ACYS X 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS X 236 " occ=0.50 Time building chain proxies: 19.00, per 1000 atoms: 0.44 Number of scatterers: 42972 At special positions: 0 Unit cell: (195.999, 195.999, 92.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 12 29.99 S 360 16.00 O 8712 8.00 N 7224 7.00 C 26664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" NE2 HIS M 79 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 141 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 134 " pdb=" ZN O1001 " pdb="ZN ZN O1001 " - pdb=" NE2 HIS O 79 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 141 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 134 " pdb=" ZN Q1001 " pdb="ZN ZN Q1001 " - pdb=" NE2 HIS Q 79 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 141 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 134 " pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" NE2 HIS S 79 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 141 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 134 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" NE2 HIS V 79 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 141 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 134 " pdb=" ZN X1001 " pdb="ZN ZN X1001 " - pdb=" NE2 HIS X 79 " pdb="ZN ZN X1001 " - pdb=" SG CYS X 141 " pdb="ZN ZN X1001 " - pdb=" SG CYS X 134 " 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10392 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 60 sheets defined 35.2% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.606A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 removed outlier: 3.665A pdb=" N ARG A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.628A pdb=" N MET A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 4.622A pdb=" N GLU A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.778A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.528A pdb=" N LEU A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 404 Processing helix chain 'A' and resid 461 through 470 removed outlier: 3.754A pdb=" N LYS A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.638A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.693A pdb=" N ARG C 41 " --> pdb=" O HIS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.608A pdb=" N MET C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 removed outlier: 4.709A pdb=" N GLU C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.770A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.503A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 363 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 404 Processing helix chain 'C' and resid 461 through 470 removed outlier: 3.747A pdb=" N LYS C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.638A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 removed outlier: 3.656A pdb=" N ARG E 41 " --> pdb=" O HIS E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.558A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 101 removed outlier: 4.592A pdb=" N GLU E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.782A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.566A pdb=" N LEU E 346 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 404 Processing helix chain 'E' and resid 461 through 470 removed outlier: 3.772A pdb=" N LYS E 469 " --> pdb=" O ARG E 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 22 removed outlier: 3.606A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 removed outlier: 3.665A pdb=" N ARG G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.628A pdb=" N MET G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 removed outlier: 4.622A pdb=" N GLU G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.779A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.527A pdb=" N LEU G 346 " --> pdb=" O THR G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 363 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 Processing helix chain 'G' and resid 461 through 470 removed outlier: 3.754A pdb=" N LYS G 469 " --> pdb=" O ARG G 465 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.634A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.691A pdb=" N ARG I 41 " --> pdb=" O HIS I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.600A pdb=" N MET I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 101 removed outlier: 4.709A pdb=" N GLU I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.771A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.504A pdb=" N LEU I 346 " --> pdb=" O THR I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 404 Processing helix chain 'I' and resid 461 through 470 removed outlier: 3.759A pdb=" N LYS I 469 " --> pdb=" O ARG I 465 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 22 removed outlier: 3.638A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.655A pdb=" N ARG K 41 " --> pdb=" O HIS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.558A pdb=" N MET K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 101 removed outlier: 4.592A pdb=" N GLU K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 104 No H-bonds generated for 'chain 'K' and resid 102 through 104' Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.784A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 343 through 348 removed outlier: 3.566A pdb=" N LEU K 346 " --> pdb=" O THR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 404 Processing helix chain 'K' and resid 461 through 470 removed outlier: 3.773A pdb=" N LYS K 469 " --> pdb=" O ARG K 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 22 removed outlier: 3.606A pdb=" N ALA M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 55 removed outlier: 3.665A pdb=" N ARG M 41 " --> pdb=" O HIS M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.628A pdb=" N MET M 72 " --> pdb=" O ALA M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 101 removed outlier: 4.622A pdb=" N GLU M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 104 No H-bonds generated for 'chain 'M' and resid 102 through 104' Processing helix chain 'M' and resid 111 through 125 Processing helix chain 'M' and resid 157 through 167 Processing helix chain 'M' and resid 180 through 185 Processing helix chain 'M' and resid 193 through 195 No H-bonds generated for 'chain 'M' and resid 193 through 195' Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.778A pdb=" N TRP M 258 " --> pdb=" O LEU M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 342 Processing helix chain 'M' and resid 343 through 348 removed outlier: 3.530A pdb=" N LEU M 346 " --> pdb=" O THR M 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 363 Processing helix chain 'M' and resid 380 through 382 No H-bonds generated for 'chain 'M' and resid 380 through 382' Processing helix chain 'M' and resid 383 through 404 Processing helix chain 'M' and resid 461 through 470 removed outlier: 3.754A pdb=" N LYS M 469 " --> pdb=" O ARG M 465 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 22 removed outlier: 3.639A pdb=" N ALA O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 55 removed outlier: 3.692A pdb=" N ARG O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 removed outlier: 3.608A pdb=" N MET O 72 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 101 removed outlier: 4.712A pdb=" N GLU O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 125 Processing helix chain 'O' and resid 157 through 167 Processing helix chain 'O' and resid 180 through 185 Processing helix chain 'O' and resid 193 through 195 No H-bonds generated for 'chain 'O' and resid 193 through 195' Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 252 through 258 removed outlier: 3.772A pdb=" N TRP O 258 " --> pdb=" O LEU O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 342 Processing helix chain 'O' and resid 343 through 348 removed outlier: 3.504A pdb=" N LEU O 346 " --> pdb=" O THR O 343 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 363 Processing helix chain 'O' and resid 380 through 382 No H-bonds generated for 'chain 'O' and resid 380 through 382' Processing helix chain 'O' and resid 383 through 404 Processing helix chain 'O' and resid 461 through 470 removed outlier: 3.760A pdb=" N LYS O 469 " --> pdb=" O ARG O 465 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 22 removed outlier: 3.639A pdb=" N ALA Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 55 removed outlier: 3.656A pdb=" N ARG Q 41 " --> pdb=" O HIS Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 72 removed outlier: 3.557A pdb=" N MET Q 72 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 101 removed outlier: 4.592A pdb=" N GLU Q 91 " --> pdb=" O ALA Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 104 No H-bonds generated for 'chain 'Q' and resid 102 through 104' Processing helix chain 'Q' and resid 111 through 125 Processing helix chain 'Q' and resid 157 through 167 Processing helix chain 'Q' and resid 180 through 185 Processing helix chain 'Q' and resid 193 through 195 No H-bonds generated for 'chain 'Q' and resid 193 through 195' Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 252 through 258 removed outlier: 3.783A pdb=" N TRP Q 258 " --> pdb=" O LEU Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 342 Processing helix chain 'Q' and resid 343 through 348 removed outlier: 3.566A pdb=" N LEU Q 346 " --> pdb=" O THR Q 343 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 363 Processing helix chain 'Q' and resid 380 through 382 No H-bonds generated for 'chain 'Q' and resid 380 through 382' Processing helix chain 'Q' and resid 383 through 404 Processing helix chain 'Q' and resid 461 through 470 removed outlier: 3.768A pdb=" N LYS Q 469 " --> pdb=" O ARG Q 465 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.607A pdb=" N ALA S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 55 removed outlier: 3.667A pdb=" N ARG S 41 " --> pdb=" O HIS S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 72 removed outlier: 3.638A pdb=" N MET S 72 " --> pdb=" O ALA S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 101 removed outlier: 4.620A pdb=" N GLU S 91 " --> pdb=" O ALA S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 104 No H-bonds generated for 'chain 'S' and resid 102 through 104' Processing helix chain 'S' and resid 111 through 125 Processing helix chain 'S' and resid 157 through 167 Processing helix chain 'S' and resid 180 through 185 Processing helix chain 'S' and resid 193 through 195 No H-bonds generated for 'chain 'S' and resid 193 through 195' Processing helix chain 'S' and resid 203 through 205 No H-bonds generated for 'chain 'S' and resid 203 through 205' Processing helix chain 'S' and resid 252 through 258 removed outlier: 3.778A pdb=" N TRP S 258 " --> pdb=" O LEU S 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 335 through 342 Processing helix chain 'S' and resid 343 through 348 removed outlier: 3.529A pdb=" N LEU S 346 " --> pdb=" O THR S 343 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 363 Processing helix chain 'S' and resid 380 through 382 No H-bonds generated for 'chain 'S' and resid 380 through 382' Processing helix chain 'S' and resid 383 through 404 Processing helix chain 'S' and resid 461 through 470 removed outlier: 3.754A pdb=" N LYS S 469 " --> pdb=" O ARG S 465 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.637A pdb=" N ALA V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 55 removed outlier: 3.693A pdb=" N ARG V 41 " --> pdb=" O HIS V 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 72 removed outlier: 3.599A pdb=" N MET V 72 " --> pdb=" O ALA V 69 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 101 removed outlier: 4.713A pdb=" N GLU V 91 " --> pdb=" O ALA V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 125 Processing helix chain 'V' and resid 157 through 167 Processing helix chain 'V' and resid 180 through 185 Processing helix chain 'V' and resid 193 through 195 No H-bonds generated for 'chain 'V' and resid 193 through 195' Processing helix chain 'V' and resid 203 through 205 No H-bonds generated for 'chain 'V' and resid 203 through 205' Processing helix chain 'V' and resid 252 through 258 removed outlier: 3.771A pdb=" N TRP V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 342 Processing helix chain 'V' and resid 343 through 348 removed outlier: 3.504A pdb=" N LEU V 346 " --> pdb=" O THR V 343 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 363 Processing helix chain 'V' and resid 380 through 382 No H-bonds generated for 'chain 'V' and resid 380 through 382' Processing helix chain 'V' and resid 383 through 404 Processing helix chain 'V' and resid 461 through 470 removed outlier: 3.746A pdb=" N LYS V 469 " --> pdb=" O ARG V 465 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 22 removed outlier: 3.637A pdb=" N ALA X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 55 removed outlier: 3.656A pdb=" N ARG X 41 " --> pdb=" O HIS X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 67 through 72 removed outlier: 3.558A pdb=" N MET X 72 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 101 removed outlier: 4.591A pdb=" N GLU X 91 " --> pdb=" O ALA X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 104 No H-bonds generated for 'chain 'X' and resid 102 through 104' Processing helix chain 'X' and resid 111 through 125 Processing helix chain 'X' and resid 157 through 167 Processing helix chain 'X' and resid 180 through 185 Processing helix chain 'X' and resid 193 through 195 No H-bonds generated for 'chain 'X' and resid 193 through 195' Processing helix chain 'X' and resid 203 through 205 No H-bonds generated for 'chain 'X' and resid 203 through 205' Processing helix chain 'X' and resid 252 through 258 removed outlier: 3.783A pdb=" N TRP X 258 " --> pdb=" O LEU X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 342 Processing helix chain 'X' and resid 343 through 348 removed outlier: 3.565A pdb=" N LEU X 346 " --> pdb=" O THR X 343 " (cutoff:3.500A) Processing helix chain 'X' and resid 351 through 363 Processing helix chain 'X' and resid 380 through 382 No H-bonds generated for 'chain 'X' and resid 380 through 382' Processing helix chain 'X' and resid 383 through 404 Processing helix chain 'X' and resid 461 through 470 removed outlier: 3.767A pdb=" N LYS X 469 " --> pdb=" O ARG X 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.381A pdb=" N VAL A 4 " --> pdb=" O GLU A 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 7.553A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 63 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 148 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL A 176 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR A 150 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE A 178 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 4.157A pdb=" N TYR A 333 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 226 removed outlier: 3.837A pdb=" N LYS A 224 " --> pdb=" O PHE X 423 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE X 423 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP X 421 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.959A pdb=" N TRP A 421 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 423 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C 224 " --> pdb=" O PHE A 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 133 through 134 removed outlier: 7.514A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP C 63 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 246 through 251 removed outlier: 4.254A pdb=" N TYR C 333 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 303 through 307 Processing sheet with id=AB2, first strand: chain 'C' and resid 414 through 415 removed outlier: 4.028A pdb=" N TRP C 421 " --> pdb=" O SER E 226 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE C 423 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS E 224 " --> pdb=" O PHE C 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 6 removed outlier: 6.321A pdb=" N VAL E 4 " --> pdb=" O GLU E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 133 through 134 removed outlier: 7.527A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP E 63 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 246 through 251 removed outlier: 4.244A pdb=" N TYR E 333 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 303 through 307 Processing sheet with id=AB7, first strand: chain 'E' and resid 414 through 415 removed outlier: 4.073A pdb=" N TRP E 421 " --> pdb=" O SER G 226 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE E 423 " --> pdb=" O LYS G 224 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS G 224 " --> pdb=" O PHE E 423 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 6 removed outlier: 6.381A pdb=" N VAL G 4 " --> pdb=" O GLU G 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 133 through 134 removed outlier: 7.553A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP G 63 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA G 148 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL G 176 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR G 150 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE G 178 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 246 through 251 removed outlier: 4.156A pdb=" N TYR G 333 " --> pdb=" O ALA G 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 303 through 307 Processing sheet with id=AC3, first strand: chain 'G' and resid 414 through 415 removed outlier: 3.955A pdb=" N TRP G 421 " --> pdb=" O SER I 226 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE G 423 " --> pdb=" O LYS I 224 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS I 224 " --> pdb=" O PHE G 423 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AC5, first strand: chain 'I' and resid 133 through 134 removed outlier: 7.505A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP I 63 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 246 through 251 removed outlier: 4.255A pdb=" N TYR I 333 " --> pdb=" O ALA I 191 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 303 through 307 Processing sheet with id=AC8, first strand: chain 'I' and resid 414 through 415 removed outlier: 4.032A pdb=" N TRP I 421 " --> pdb=" O SER K 226 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE I 423 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS K 224 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.376A pdb=" N VAL K 4 " --> pdb=" O GLU K 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'K' and resid 133 through 134 removed outlier: 7.532A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP K 63 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 246 through 251 removed outlier: 4.245A pdb=" N TYR K 333 " --> pdb=" O ALA K 191 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 303 through 307 Processing sheet with id=AD4, first strand: chain 'K' and resid 414 through 415 removed outlier: 4.071A pdb=" N TRP K 421 " --> pdb=" O SER M 226 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE K 423 " --> pdb=" O LYS M 224 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS M 224 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 4 through 6 removed outlier: 6.380A pdb=" N VAL M 4 " --> pdb=" O GLU M 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'M' and resid 133 through 134 removed outlier: 7.553A pdb=" N CYS M 134 " --> pdb=" O TYR M 78 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N CYS M 80 " --> pdb=" O CYS M 134 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP M 63 " --> pdb=" O HIS M 79 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN M 151 " --> pdb=" O ILE M 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA M 148 " --> pdb=" O TYR M 174 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL M 176 " --> pdb=" O ALA M 148 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR M 150 " --> pdb=" O VAL M 176 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE M 178 " --> pdb=" O TYR M 150 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TYR M 285 " --> pdb=" O SER M 281 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER M 281 " --> pdb=" O TYR M 285 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL M 287 " --> pdb=" O VAL M 279 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 246 through 251 removed outlier: 4.156A pdb=" N TYR M 333 " --> pdb=" O ALA M 191 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 303 through 307 Processing sheet with id=AD9, first strand: chain 'M' and resid 414 through 415 removed outlier: 3.957A pdb=" N TRP M 421 " --> pdb=" O SER O 226 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE M 423 " --> pdb=" O LYS O 224 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS O 224 " --> pdb=" O PHE M 423 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AE2, first strand: chain 'O' and resid 133 through 134 removed outlier: 7.505A pdb=" N CYS O 134 " --> pdb=" O TYR O 78 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS O 80 " --> pdb=" O CYS O 134 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP O 63 " --> pdb=" O HIS O 79 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN O 151 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR O 285 " --> pdb=" O SER O 281 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER O 281 " --> pdb=" O TYR O 285 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL O 287 " --> pdb=" O VAL O 279 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 246 through 251 removed outlier: 4.254A pdb=" N TYR O 333 " --> pdb=" O ALA O 191 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 303 through 307 Processing sheet with id=AE5, first strand: chain 'O' and resid 414 through 415 removed outlier: 4.028A pdb=" N TRP O 421 " --> pdb=" O SER Q 226 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE O 423 " --> pdb=" O LYS Q 224 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS Q 224 " --> pdb=" O PHE O 423 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 4 through 6 removed outlier: 6.313A pdb=" N VAL Q 4 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'Q' and resid 133 through 134 removed outlier: 7.529A pdb=" N CYS Q 134 " --> pdb=" O TYR Q 78 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS Q 80 " --> pdb=" O CYS Q 134 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP Q 63 " --> pdb=" O HIS Q 79 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN Q 151 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR Q 285 " --> pdb=" O SER Q 281 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER Q 281 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL Q 287 " --> pdb=" O VAL Q 279 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 246 through 251 removed outlier: 4.244A pdb=" N TYR Q 333 " --> pdb=" O ALA Q 191 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 303 through 307 Processing sheet with id=AF1, first strand: chain 'Q' and resid 414 through 415 removed outlier: 4.068A pdb=" N TRP Q 421 " --> pdb=" O SER S 226 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE Q 423 " --> pdb=" O LYS S 224 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS S 224 " --> pdb=" O PHE Q 423 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 4 through 6 removed outlier: 6.380A pdb=" N VAL S 4 " --> pdb=" O GLU S 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'S' and resid 133 through 134 removed outlier: 7.554A pdb=" N CYS S 134 " --> pdb=" O TYR S 78 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N CYS S 80 " --> pdb=" O CYS S 134 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP S 63 " --> pdb=" O HIS S 79 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN S 151 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA S 148 " --> pdb=" O TYR S 174 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL S 176 " --> pdb=" O ALA S 148 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR S 150 " --> pdb=" O VAL S 176 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE S 178 " --> pdb=" O TYR S 150 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER S 281 " --> pdb=" O TYR S 285 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL S 287 " --> pdb=" O VAL S 279 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 246 through 251 removed outlier: 4.156A pdb=" N TYR S 333 " --> pdb=" O ALA S 191 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 303 through 307 Processing sheet with id=AF6, first strand: chain 'S' and resid 414 through 415 removed outlier: 3.960A pdb=" N TRP S 421 " --> pdb=" O SER V 226 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE S 423 " --> pdb=" O LYS V 224 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS V 224 " --> pdb=" O PHE S 423 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 5 through 6 Processing sheet with id=AF8, first strand: chain 'V' and resid 133 through 134 removed outlier: 7.510A pdb=" N CYS V 134 " --> pdb=" O TYR V 78 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS V 80 " --> pdb=" O CYS V 134 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP V 63 " --> pdb=" O HIS V 79 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN V 151 " --> pdb=" O ILE V 64 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR V 285 " --> pdb=" O SER V 281 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER V 281 " --> pdb=" O TYR V 285 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL V 287 " --> pdb=" O VAL V 279 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 246 through 251 removed outlier: 4.254A pdb=" N TYR V 333 " --> pdb=" O ALA V 191 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 303 through 307 Processing sheet with id=AG2, first strand: chain 'V' and resid 414 through 415 removed outlier: 4.026A pdb=" N TRP V 421 " --> pdb=" O SER X 226 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE V 423 " --> pdb=" O LYS X 224 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS X 224 " --> pdb=" O PHE V 423 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 4 through 6 removed outlier: 6.366A pdb=" N VAL X 4 " --> pdb=" O GLU X 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'X' and resid 133 through 134 removed outlier: 7.518A pdb=" N CYS X 134 " --> pdb=" O TYR X 78 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS X 80 " --> pdb=" O CYS X 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP X 63 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN X 151 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR X 285 " --> pdb=" O SER X 281 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER X 281 " --> pdb=" O TYR X 285 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL X 287 " --> pdb=" O VAL X 279 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 246 through 251 removed outlier: 4.244A pdb=" N TYR X 333 " --> pdb=" O ALA X 191 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 303 through 307 1896 hydrogen bonds defined for protein. 5268 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: 14.26 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13282 1.34 - 1.46: 10273 1.46 - 1.59: 18913 1.59 - 1.71: 0 1.71 - 1.84: 516 Bond restraints: 42984 Sorted by residual: bond pdb=" C ILE X 462 " pdb=" N PRO X 463 " ideal model delta sigma weight residual 1.333 1.370 -0.037 1.44e-02 4.82e+03 6.50e+00 bond pdb=" C ILE E 462 " pdb=" N PRO E 463 " ideal model delta sigma weight residual 1.333 1.370 -0.036 1.44e-02 4.82e+03 6.38e+00 bond pdb=" C ILE V 462 " pdb=" N PRO V 463 " ideal model delta sigma weight residual 1.333 1.370 -0.036 1.44e-02 4.82e+03 6.37e+00 bond pdb=" C ILE Q 462 " pdb=" N PRO Q 463 " ideal model delta sigma weight residual 1.333 1.370 -0.036 1.44e-02 4.82e+03 6.37e+00 bond pdb=" C ILE C 462 " pdb=" N PRO C 463 " ideal model delta sigma weight residual 1.333 1.370 -0.036 1.44e-02 4.82e+03 6.36e+00 ... (remaining 42979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 55921 1.86 - 3.73: 2123 3.73 - 5.59: 312 5.59 - 7.45: 60 7.45 - 9.32: 12 Bond angle restraints: 58428 Sorted by residual: angle pdb=" C GLU X 219 " pdb=" CA GLU X 219 " pdb=" CB GLU X 219 " ideal model delta sigma weight residual 109.83 105.61 4.22 9.90e-01 1.02e+00 1.81e+01 angle pdb=" C GLU E 219 " pdb=" CA GLU E 219 " pdb=" CB GLU E 219 " ideal model delta sigma weight residual 109.83 105.63 4.20 9.90e-01 1.02e+00 1.80e+01 angle pdb=" C GLU Q 219 " pdb=" CA GLU Q 219 " pdb=" CB GLU Q 219 " ideal model delta sigma weight residual 109.83 105.66 4.17 9.90e-01 1.02e+00 1.78e+01 angle pdb=" C GLU K 219 " pdb=" CA GLU K 219 " pdb=" CB GLU K 219 " ideal model delta sigma weight residual 109.83 105.69 4.14 9.90e-01 1.02e+00 1.75e+01 angle pdb=" C GLU O 219 " pdb=" CA GLU O 219 " pdb=" CB GLU O 219 " ideal model delta sigma weight residual 109.83 106.01 3.82 9.90e-01 1.02e+00 1.49e+01 ... (remaining 58423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 23964 17.86 - 35.72: 1711 35.72 - 53.58: 292 53.58 - 71.44: 36 71.44 - 89.30: 49 Dihedral angle restraints: 26052 sinusoidal: 9948 harmonic: 16104 Sorted by residual: dihedral pdb=" CA GLN X 444 " pdb=" C GLN X 444 " pdb=" N ALA X 445 " pdb=" CA ALA X 445 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLN E 444 " pdb=" C GLN E 444 " pdb=" N ALA E 445 " pdb=" CA ALA E 445 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLN Q 444 " pdb=" C GLN Q 444 " pdb=" N ALA Q 445 " pdb=" CA ALA Q 445 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 26049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 5351 0.074 - 0.148: 1243 0.148 - 0.223: 82 0.223 - 0.297: 8 0.297 - 0.371: 12 Chirality restraints: 6696 Sorted by residual: chirality pdb=" CB ILE Q 462 " pdb=" CA ILE Q 462 " pdb=" CG1 ILE Q 462 " pdb=" CG2 ILE Q 462 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB ILE X 462 " pdb=" CA ILE X 462 " pdb=" CG1 ILE X 462 " pdb=" CG2 ILE X 462 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB ILE E 462 " pdb=" CA ILE E 462 " pdb=" CG1 ILE E 462 " pdb=" CG2 ILE E 462 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 6693 not shown) Planarity restraints: 7416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 285 " 0.015 2.00e-02 2.50e+03 2.19e-02 9.56e+00 pdb=" CG TYR Q 285 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 285 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 285 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 285 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 285 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR Q 285 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR Q 285 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR X 285 " -0.015 2.00e-02 2.50e+03 2.19e-02 9.55e+00 pdb=" CG TYR X 285 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR X 285 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR X 285 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR X 285 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR X 285 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR X 285 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR X 285 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 285 " 0.015 2.00e-02 2.50e+03 2.18e-02 9.55e+00 pdb=" CG TYR K 285 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR K 285 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR K 285 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR K 285 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR K 285 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR K 285 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR K 285 " 0.001 2.00e-02 2.50e+03 ... (remaining 7413 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 344 2.43 - 3.05: 26272 3.05 - 3.67: 67847 3.67 - 4.28: 112011 4.28 - 4.90: 175214 Nonbonded interactions: 381688 Sorted by model distance: nonbonded pdb=" OE2 GLU A 129 " pdb="ZN ZN A1001 " model vdw 1.818 2.230 nonbonded pdb=" OE2 GLU M 129 " pdb="ZN ZN M1001 " model vdw 1.820 2.230 nonbonded pdb=" OE2 GLU G 129 " pdb="ZN ZN G1001 " model vdw 1.820 2.230 nonbonded pdb=" OE2 GLU S 129 " pdb="ZN ZN S1001 " model vdw 1.820 2.230 nonbonded pdb=" OE2 GLU O 129 " pdb="ZN ZN O1001 " model vdw 1.826 2.230 ... (remaining 381683 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'C' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'E' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'G' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'I' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'K' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'M' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'O' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'Q' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'S' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'V' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) selection = (chain 'X' and (resid 3 through 19 or resid 21 through 235 or resid 237 through \ 247 or resid 249 through 352 or resid 354 through 1001)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 60.120 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.130 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 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 : 0.011 0.356 43020 Z= 0.465 Angle : 0.872 9.317 58428 Z= 0.481 Chirality : 0.061 0.371 6696 Planarity : 0.006 0.042 7416 Dihedral : 13.087 89.304 15660 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.27 % Allowed : 1.23 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.69 (0.09), residues: 5424 helix: -1.63 (0.11), residues: 1680 sheet: 0.28 (0.15), residues: 1020 loop : -2.78 (0.09), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 110 TYR 0.052 0.004 TYR X 285 PHE 0.021 0.003 PHE E 183 TRP 0.016 0.003 TRP O 258 HIS 0.006 0.002 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00964 (42984) covalent geometry : angle 0.87155 (58428) hydrogen bonds : bond 0.16148 ( 1896) hydrogen bonds : angle 6.88127 ( 5268) metal coordination : bond 0.21409 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 1.587 Fit side-chains REVERT: A 49 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8186 (mmpt) REVERT: A 400 LYS cc_start: 0.7976 (mttt) cc_final: 0.7673 (mttp) REVERT: C 49 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8124 (mmpt) REVERT: C 73 MET cc_start: 0.6249 (mmm) cc_final: 0.5851 (mmt) REVERT: C 250 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6992 (tp30) REVERT: E 49 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8111 (mmpt) REVERT: E 400 LYS cc_start: 0.8035 (mttt) cc_final: 0.7720 (mttp) REVERT: G 26 GLU cc_start: 0.7283 (tm-30) cc_final: 0.7030 (tm-30) REVERT: G 49 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8193 (mmpt) REVERT: G 400 LYS cc_start: 0.7984 (mttt) cc_final: 0.7683 (mttp) REVERT: I 49 LYS cc_start: 0.8363 (mmtt) cc_final: 0.8123 (mmpt) REVERT: I 73 MET cc_start: 0.6248 (mmm) cc_final: 0.5852 (mmt) REVERT: I 250 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6990 (tp30) REVERT: K 49 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8107 (mmpt) REVERT: K 400 LYS cc_start: 0.8031 (mttt) cc_final: 0.7714 (mttp) REVERT: M 26 GLU cc_start: 0.7253 (tm-30) cc_final: 0.7001 (tm-30) REVERT: M 400 LYS cc_start: 0.7993 (mttt) cc_final: 0.7698 (mttp) REVERT: O 49 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8128 (mmpt) REVERT: O 54 GLU cc_start: 0.7311 (tt0) cc_final: 0.7000 (tm-30) REVERT: O 73 MET cc_start: 0.6264 (mmm) cc_final: 0.5864 (mmt) REVERT: Q 26 GLU cc_start: 0.7135 (tp30) cc_final: 0.6841 (mp0) REVERT: Q 49 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8108 (mmpt) REVERT: Q 400 LYS cc_start: 0.8032 (mttt) cc_final: 0.7717 (mttp) REVERT: S 26 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6990 (tm-30) REVERT: S 49 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8185 (mmpt) REVERT: S 400 LYS cc_start: 0.7964 (mttt) cc_final: 0.7670 (mttp) REVERT: V 49 LYS cc_start: 0.8362 (mmtt) cc_final: 0.8127 (mmpt) REVERT: V 73 MET cc_start: 0.6244 (mmm) cc_final: 0.5849 (mmt) REVERT: V 250 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6992 (tp30) REVERT: X 26 GLU cc_start: 0.7137 (tp30) cc_final: 0.6847 (mp0) REVERT: X 49 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8107 (mmpt) REVERT: X 400 LYS cc_start: 0.8030 (mttt) cc_final: 0.7713 (mttp) outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.8199 time to fit residues: 611.2559 Evaluate side-chains 510 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 2.9990 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 0.0870 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 389 GLN C 111 ASN C 203 GLN E 203 GLN E 389 GLN G 203 GLN G 389 GLN I 111 ASN I 203 GLN K 203 GLN K 389 GLN M 203 GLN M 389 GLN O 111 ASN O 203 GLN Q 203 GLN S 203 GLN S 389 GLN V 111 ASN V 203 GLN X 203 GLN X 389 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.178560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.139331 restraints weight = 139137.332| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.33 r_work: 0.2925 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43020 Z= 0.132 Angle : 0.590 5.974 58428 Z= 0.308 Chirality : 0.045 0.297 6696 Planarity : 0.004 0.036 7416 Dihedral : 5.074 21.327 5988 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.78 % Allowed : 4.12 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.10), residues: 5424 helix: 0.47 (0.12), residues: 1752 sheet: 0.32 (0.15), residues: 1140 loop : -2.62 (0.09), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 71 TYR 0.011 0.001 TYR G 382 PHE 0.015 0.002 PHE O 264 TRP 0.009 0.001 TRP O 258 HIS 0.005 0.001 HIS X 79 Details of bonding type rmsd covalent geometry : bond 0.00307 (42984) covalent geometry : angle 0.58951 (58428) hydrogen bonds : bond 0.03608 ( 1896) hydrogen bonds : angle 4.72744 ( 5268) metal coordination : bond 0.00684 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 558 time to evaluate : 1.645 Fit side-chains REVERT: A 49 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8283 (mmpt) REVERT: A 54 GLU cc_start: 0.7813 (tt0) cc_final: 0.7167 (tm-30) REVERT: A 277 ASP cc_start: 0.8544 (m-30) cc_final: 0.8344 (p0) REVERT: A 400 LYS cc_start: 0.8625 (mttt) cc_final: 0.8415 (mtmp) REVERT: A 403 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 49 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8131 (mmpt) REVERT: C 54 GLU cc_start: 0.7528 (tt0) cc_final: 0.7242 (tm-30) REVERT: C 250 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7782 (tp30) REVERT: C 277 ASP cc_start: 0.8622 (m-30) cc_final: 0.8405 (p0) REVERT: C 402 MET cc_start: 0.8632 (mtm) cc_final: 0.8400 (ttm) REVERT: C 448 ASP cc_start: 0.8159 (p0) cc_final: 0.7902 (t0) REVERT: E 49 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8173 (mmpt) REVERT: E 54 GLU cc_start: 0.7535 (tt0) cc_final: 0.7107 (tm-30) REVERT: E 89 ASP cc_start: 0.6763 (m-30) cc_final: 0.6544 (m-30) REVERT: E 314 MET cc_start: 0.8898 (ttt) cc_final: 0.8687 (ttt) REVERT: G 26 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7477 (tm-30) REVERT: G 49 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8269 (mmpt) REVERT: G 54 GLU cc_start: 0.7821 (tt0) cc_final: 0.7175 (tm-30) REVERT: G 400 LYS cc_start: 0.8604 (mttt) cc_final: 0.8400 (mtmp) REVERT: G 403 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7616 (mt-10) REVERT: I 26 GLU cc_start: 0.6991 (mp0) cc_final: 0.6727 (mm-30) REVERT: I 49 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8145 (mmpt) REVERT: I 54 GLU cc_start: 0.7632 (tt0) cc_final: 0.7279 (tm-30) REVERT: I 250 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7794 (tp30) REVERT: I 277 ASP cc_start: 0.8625 (m-30) cc_final: 0.8399 (p0) REVERT: I 402 MET cc_start: 0.8645 (mtm) cc_final: 0.8416 (ttm) REVERT: I 448 ASP cc_start: 0.8153 (p0) cc_final: 0.7923 (t0) REVERT: K 49 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8184 (mmpt) REVERT: K 54 GLU cc_start: 0.7572 (tt0) cc_final: 0.7122 (tm-30) REVERT: K 89 ASP cc_start: 0.6759 (m-30) cc_final: 0.6541 (m-30) REVERT: K 314 MET cc_start: 0.8897 (ttt) cc_final: 0.8683 (ttt) REVERT: M 26 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7470 (tm-30) REVERT: M 54 GLU cc_start: 0.7805 (tt0) cc_final: 0.7151 (tm-30) REVERT: M 400 LYS cc_start: 0.8616 (mttt) cc_final: 0.8413 (mtmp) REVERT: M 403 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7620 (mt-10) REVERT: O 26 GLU cc_start: 0.6988 (mp0) cc_final: 0.6714 (mm-30) REVERT: O 49 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8137 (mmpt) REVERT: O 54 GLU cc_start: 0.7585 (tt0) cc_final: 0.7007 (tm-30) REVERT: O 448 ASP cc_start: 0.8179 (p0) cc_final: 0.7940 (t0) REVERT: Q 26 GLU cc_start: 0.7699 (tp30) cc_final: 0.7035 (mp0) REVERT: Q 49 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8194 (mmpt) REVERT: Q 54 GLU cc_start: 0.7599 (tt0) cc_final: 0.7133 (tm-30) REVERT: Q 89 ASP cc_start: 0.6790 (m-30) cc_final: 0.6568 (m-30) REVERT: S 26 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7434 (tm-30) REVERT: S 49 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8287 (mmpt) REVERT: S 54 GLU cc_start: 0.7786 (tt0) cc_final: 0.7146 (tm-30) REVERT: S 400 LYS cc_start: 0.8619 (mttt) cc_final: 0.8415 (mtmp) REVERT: S 403 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7621 (mt-10) REVERT: V 26 GLU cc_start: 0.6982 (mp0) cc_final: 0.6706 (mm-30) REVERT: V 49 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8144 (mmpt) REVERT: V 54 GLU cc_start: 0.7658 (tt0) cc_final: 0.7283 (tm-30) REVERT: V 250 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7773 (tp30) REVERT: V 402 MET cc_start: 0.8650 (mtm) cc_final: 0.8431 (ttm) REVERT: V 448 ASP cc_start: 0.8193 (p0) cc_final: 0.7930 (t0) REVERT: X 26 GLU cc_start: 0.7705 (tp30) cc_final: 0.7047 (mp0) REVERT: X 49 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8194 (mmpt) REVERT: X 54 GLU cc_start: 0.7511 (tt0) cc_final: 0.7097 (tm-30) REVERT: X 89 ASP cc_start: 0.6800 (m-30) cc_final: 0.6579 (m-30) REVERT: X 314 MET cc_start: 0.8897 (ttt) cc_final: 0.8684 (ttt) REVERT: X 402 MET cc_start: 0.8603 (mtm) cc_final: 0.8155 (ttm) outliers start: 23 outliers final: 4 residues processed: 569 average time/residue: 0.9628 time to fit residues: 651.4232 Evaluate side-chains 527 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 523 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain X residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 176 optimal weight: 4.9990 chunk 335 optimal weight: 0.0570 chunk 83 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 333 optimal weight: 8.9990 chunk 363 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 chunk 496 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 452 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN C 151 GLN E 151 GLN G 151 GLN I 151 GLN K 151 GLN M 151 GLN O 151 GLN Q 151 GLN S 151 GLN V 151 GLN X 151 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.179908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.139805 restraints weight = 153140.488| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.54 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43020 Z= 0.114 Angle : 0.540 10.196 58428 Z= 0.279 Chirality : 0.043 0.245 6696 Planarity : 0.004 0.031 7416 Dihedral : 4.547 17.920 5988 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.96 % Allowed : 5.46 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.11), residues: 5424 helix: 1.56 (0.13), residues: 1740 sheet: 0.52 (0.15), residues: 1140 loop : -2.30 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 76 TYR 0.010 0.001 TYR S 382 PHE 0.013 0.001 PHE I 264 TRP 0.007 0.001 TRP O 258 HIS 0.004 0.001 HIS G 164 Details of bonding type rmsd covalent geometry : bond 0.00266 (42984) covalent geometry : angle 0.54012 (58428) hydrogen bonds : bond 0.03206 ( 1896) hydrogen bonds : angle 4.39496 ( 5268) metal coordination : bond 0.00503 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 536 time to evaluate : 1.636 Fit side-chains REVERT: A 403 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7133 (mt-10) REVERT: C 26 GLU cc_start: 0.6593 (mp0) cc_final: 0.6285 (mp0) REVERT: C 402 MET cc_start: 0.7990 (mtm) cc_final: 0.7785 (ttm) REVERT: E 314 MET cc_start: 0.8347 (ttt) cc_final: 0.8034 (ttt) REVERT: E 320 THR cc_start: 0.8603 (p) cc_final: 0.8362 (p) REVERT: G 403 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7097 (mt-10) REVERT: K 314 MET cc_start: 0.8349 (ttt) cc_final: 0.8033 (ttt) REVERT: K 320 THR cc_start: 0.8600 (p) cc_final: 0.8362 (p) REVERT: M 72 MET cc_start: 0.6925 (ttp) cc_final: 0.6698 (tmm) REVERT: M 403 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7117 (mt-10) REVERT: O 26 GLU cc_start: 0.6576 (mp0) cc_final: 0.6306 (mp0) REVERT: Q 314 MET cc_start: 0.8408 (ttt) cc_final: 0.7882 (ttt) REVERT: Q 320 THR cc_start: 0.8594 (p) cc_final: 0.8347 (p) REVERT: S 403 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7103 (mt-10) REVERT: V 26 GLU cc_start: 0.6563 (mp0) cc_final: 0.6283 (mp0) REVERT: X 314 MET cc_start: 0.8467 (ttt) cc_final: 0.8156 (ttt) REVERT: X 320 THR cc_start: 0.8594 (p) cc_final: 0.8350 (p) REVERT: X 402 MET cc_start: 0.7891 (mtm) cc_final: 0.7477 (ttm) outliers start: 31 outliers final: 4 residues processed: 559 average time/residue: 0.8675 time to fit residues: 582.4481 Evaluate side-chains 492 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 488 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain X residue 156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 399 optimal weight: 0.0040 chunk 486 optimal weight: 4.9990 chunk 512 optimal weight: 9.9990 chunk 471 optimal weight: 0.9990 chunk 515 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 259 optimal weight: 0.2980 chunk 245 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN C 151 GLN G 151 GLN I 151 GLN M 151 GLN O 151 GLN S 151 GLN V 151 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.182341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.136893 restraints weight = 137341.616| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.60 r_work: 0.2955 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 43020 Z= 0.102 Angle : 0.525 10.435 58428 Z= 0.270 Chirality : 0.043 0.211 6696 Planarity : 0.004 0.030 7416 Dihedral : 4.271 16.618 5988 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.85 % Allowed : 7.06 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.11), residues: 5424 helix: 1.99 (0.13), residues: 1752 sheet: 0.54 (0.15), residues: 1164 loop : -2.06 (0.10), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 275 TYR 0.009 0.001 TYR G 382 PHE 0.012 0.001 PHE V 264 TRP 0.006 0.001 TRP C 258 HIS 0.003 0.001 HIS S 79 Details of bonding type rmsd covalent geometry : bond 0.00237 (42984) covalent geometry : angle 0.52529 (58428) hydrogen bonds : bond 0.02812 ( 1896) hydrogen bonds : angle 4.20017 ( 5268) metal coordination : bond 0.00146 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 514 time to evaluate : 1.549 Fit side-chains REVERT: A 151 GLN cc_start: 0.8901 (tt0) cc_final: 0.8699 (tt0) REVERT: A 403 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 26 GLU cc_start: 0.6967 (mp0) cc_final: 0.6565 (mp0) REVERT: C 73 MET cc_start: 0.6405 (mmm) cc_final: 0.5791 (mmm) REVERT: C 123 MET cc_start: 0.5052 (mmp) cc_final: 0.4775 (mmm) REVERT: C 402 MET cc_start: 0.8615 (mtm) cc_final: 0.8395 (ttm) REVERT: C 448 ASP cc_start: 0.7744 (t0) cc_final: 0.7481 (m-30) REVERT: E 26 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6963 (mp0) REVERT: E 73 MET cc_start: 0.6398 (mmm) cc_final: 0.6128 (mmm) REVERT: E 275 ARG cc_start: 0.8464 (mtm110) cc_final: 0.8128 (mtp-110) REVERT: E 314 MET cc_start: 0.8898 (ttt) cc_final: 0.8686 (ttt) REVERT: E 400 LYS cc_start: 0.8499 (mttp) cc_final: 0.8239 (mttt) REVERT: E 402 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8207 (ttm) REVERT: E 448 ASP cc_start: 0.8014 (t0) cc_final: 0.7702 (m-30) REVERT: G 151 GLN cc_start: 0.8895 (tt0) cc_final: 0.8678 (tt0) REVERT: G 403 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7658 (mt-10) REVERT: I 73 MET cc_start: 0.6435 (mmm) cc_final: 0.5834 (mmm) REVERT: K 26 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6923 (mp0) REVERT: K 73 MET cc_start: 0.6408 (mmm) cc_final: 0.6104 (mmm) REVERT: K 275 ARG cc_start: 0.8433 (mtm110) cc_final: 0.8102 (mtp-110) REVERT: K 314 MET cc_start: 0.8905 (ttt) cc_final: 0.8699 (ttt) REVERT: K 402 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8226 (ttm) REVERT: K 448 ASP cc_start: 0.8021 (t0) cc_final: 0.7698 (m-30) REVERT: M 403 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7620 (mt-10) REVERT: O 26 GLU cc_start: 0.6980 (mp0) cc_final: 0.6586 (mp0) REVERT: O 73 MET cc_start: 0.6395 (mmm) cc_final: 0.5793 (mmm) REVERT: O 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.6052 (m-30) REVERT: O 292 MET cc_start: 0.8615 (mtm) cc_final: 0.8365 (mtm) REVERT: Q 26 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6857 (mp0) REVERT: Q 73 MET cc_start: 0.6413 (mmm) cc_final: 0.6109 (mmm) REVERT: Q 275 ARG cc_start: 0.8455 (mtm110) cc_final: 0.8126 (mtp-110) REVERT: Q 314 MET cc_start: 0.8912 (ttt) cc_final: 0.8593 (ttt) REVERT: Q 402 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8214 (ttm) REVERT: Q 448 ASP cc_start: 0.7980 (t0) cc_final: 0.7666 (m-30) REVERT: S 151 GLN cc_start: 0.8902 (tt0) cc_final: 0.8695 (tt0) REVERT: S 403 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7656 (mt-10) REVERT: V 26 GLU cc_start: 0.6931 (mp0) cc_final: 0.6536 (mp0) REVERT: V 73 MET cc_start: 0.6290 (mmm) cc_final: 0.6046 (mmm) REVERT: V 123 MET cc_start: 0.5077 (mmp) cc_final: 0.4803 (mmm) REVERT: V 292 MET cc_start: 0.8602 (mtm) cc_final: 0.8326 (mtm) REVERT: V 448 ASP cc_start: 0.7737 (t0) cc_final: 0.7464 (m-30) REVERT: X 73 MET cc_start: 0.6398 (mmm) cc_final: 0.6122 (mmm) REVERT: X 275 ARG cc_start: 0.8451 (mtm110) cc_final: 0.8114 (mtp-110) REVERT: X 314 MET cc_start: 0.8893 (ttt) cc_final: 0.8682 (ttt) REVERT: X 448 ASP cc_start: 0.8001 (t0) cc_final: 0.7682 (m-30) outliers start: 26 outliers final: 4 residues processed: 533 average time/residue: 0.8622 time to fit residues: 550.7675 Evaluate side-chains 482 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 475 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 402 MET Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 402 MET Chi-restraints excluded: chain X residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 45 optimal weight: 10.0000 chunk 489 optimal weight: 8.9990 chunk 466 optimal weight: 10.0000 chunk 478 optimal weight: 9.9990 chunk 227 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 519 optimal weight: 0.8980 chunk 397 optimal weight: 5.9990 chunk 440 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 151 GLN E 19 GLN E 151 GLN I 19 GLN I 151 GLN K 151 GLN M 151 GLN O 19 GLN O 151 GLN Q 151 GLN V 19 GLN X 151 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.176893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.130183 restraints weight = 137549.355| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.60 r_work: 0.2816 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43020 Z= 0.164 Angle : 0.592 6.369 58428 Z= 0.305 Chirality : 0.046 0.216 6696 Planarity : 0.004 0.030 7416 Dihedral : 4.665 20.587 5988 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.05 % Allowed : 8.53 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.11), residues: 5424 helix: 2.00 (0.13), residues: 1752 sheet: 0.60 (0.16), residues: 1044 loop : -1.96 (0.10), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 275 TYR 0.013 0.001 TYR I 150 PHE 0.014 0.001 PHE M 183 TRP 0.010 0.001 TRP X 258 HIS 0.005 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00386 (42984) covalent geometry : angle 0.59161 (58428) hydrogen bonds : bond 0.03625 ( 1896) hydrogen bonds : angle 4.34310 ( 5268) metal coordination : bond 0.00776 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 508 time to evaluate : 1.619 Fit side-chains REVERT: A 54 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6267 (mm-30) REVERT: A 403 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 427 LYS cc_start: 0.8759 (pttm) cc_final: 0.8533 (pttt) REVERT: C 26 GLU cc_start: 0.6982 (mp0) cc_final: 0.6594 (mp0) REVERT: C 73 MET cc_start: 0.6335 (mmm) cc_final: 0.5723 (mmm) REVERT: C 123 MET cc_start: 0.5103 (mmp) cc_final: 0.4797 (mmm) REVERT: C 250 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8033 (mm-30) REVERT: C 448 ASP cc_start: 0.7847 (t0) cc_final: 0.7577 (m-30) REVERT: E 275 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8083 (mtp-110) REVERT: E 448 ASP cc_start: 0.8134 (t0) cc_final: 0.7867 (m-30) REVERT: G 54 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6285 (mm-30) REVERT: G 403 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7733 (mt-10) REVERT: G 427 LYS cc_start: 0.8757 (pttm) cc_final: 0.8536 (pttt) REVERT: I 73 MET cc_start: 0.6337 (mmm) cc_final: 0.5715 (mmm) REVERT: I 123 MET cc_start: 0.5171 (mmp) cc_final: 0.4901 (mmm) REVERT: I 250 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8044 (mm-30) REVERT: I 448 ASP cc_start: 0.7805 (t0) cc_final: 0.7562 (m-30) REVERT: K 275 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8076 (mtp-110) REVERT: K 448 ASP cc_start: 0.8118 (t0) cc_final: 0.7849 (m-30) REVERT: M 403 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7728 (mt-10) REVERT: M 427 LYS cc_start: 0.8754 (pttm) cc_final: 0.8530 (pttt) REVERT: O 26 GLU cc_start: 0.7002 (mp0) cc_final: 0.6680 (mp0) REVERT: O 73 MET cc_start: 0.6328 (mmm) cc_final: 0.5715 (mmm) REVERT: O 89 ASP cc_start: 0.6493 (m-30) cc_final: 0.6200 (m-30) REVERT: O 123 MET cc_start: 0.5174 (mmp) cc_final: 0.4906 (mmm) REVERT: O 277 ASP cc_start: 0.8579 (m-30) cc_final: 0.8371 (p0) REVERT: O 448 ASP cc_start: 0.7813 (t0) cc_final: 0.7572 (m-30) REVERT: Q 275 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8085 (mtp-110) REVERT: Q 314 MET cc_start: 0.8991 (ttt) cc_final: 0.8719 (ttt) REVERT: Q 448 ASP cc_start: 0.8133 (t0) cc_final: 0.7869 (m-30) REVERT: S 54 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6301 (mm-30) REVERT: S 72 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7018 (ttp) REVERT: S 403 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7727 (mt-10) REVERT: S 427 LYS cc_start: 0.8750 (pttm) cc_final: 0.8526 (pttt) REVERT: V 26 GLU cc_start: 0.6982 (mp0) cc_final: 0.6602 (mp0) REVERT: V 73 MET cc_start: 0.6285 (mmm) cc_final: 0.6002 (mmm) REVERT: V 123 MET cc_start: 0.5157 (mmp) cc_final: 0.4868 (mmm) REVERT: V 250 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8039 (mm-30) REVERT: V 277 ASP cc_start: 0.8575 (m-30) cc_final: 0.8361 (p0) REVERT: V 448 ASP cc_start: 0.7843 (t0) cc_final: 0.7572 (m-30) REVERT: X 275 ARG cc_start: 0.8464 (mtm110) cc_final: 0.8083 (mtp-110) REVERT: X 448 ASP cc_start: 0.8131 (t0) cc_final: 0.7866 (m-30) outliers start: 35 outliers final: 4 residues processed: 537 average time/residue: 0.9215 time to fit residues: 589.3194 Evaluate side-chains 512 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 507 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain S residue 72 MET Chi-restraints excluded: chain X residue 156 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 439 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 322 optimal weight: 20.0000 chunk 375 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 216 optimal weight: 0.7980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 151 GLN E 151 GLN I 151 GLN K 151 GLN M 151 GLN O 151 GLN Q 151 GLN X 151 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.177188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130966 restraints weight = 140598.570| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.66 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43020 Z= 0.151 Angle : 0.577 5.632 58428 Z= 0.299 Chirality : 0.045 0.143 6696 Planarity : 0.004 0.031 7416 Dihedral : 4.653 20.446 5988 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.98 % Allowed : 9.20 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.11), residues: 5424 helix: 2.11 (0.13), residues: 1752 sheet: 0.59 (0.16), residues: 1044 loop : -1.90 (0.10), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 275 TYR 0.013 0.001 TYR C 150 PHE 0.014 0.001 PHE Q 183 TRP 0.008 0.001 TRP K 258 HIS 0.005 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00357 (42984) covalent geometry : angle 0.57695 (58428) hydrogen bonds : bond 0.03493 ( 1896) hydrogen bonds : angle 4.30849 ( 5268) metal coordination : bond 0.00594 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 514 time to evaluate : 1.528 Fit side-chains REVERT: A 403 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7197 (mt-10) REVERT: C 26 GLU cc_start: 0.6596 (mp0) cc_final: 0.6325 (mp0) REVERT: E 26 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6813 (mp0) REVERT: E 314 MET cc_start: 0.8489 (ttt) cc_final: 0.8036 (ttt) REVERT: G 403 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7221 (mt-10) REVERT: K 26 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6814 (mp0) REVERT: K 314 MET cc_start: 0.8471 (ttt) cc_final: 0.8024 (ttt) REVERT: M 70 ARG cc_start: 0.7724 (ptt180) cc_final: 0.7476 (ptt90) REVERT: M 403 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7217 (mt-10) REVERT: O 26 GLU cc_start: 0.6598 (mp0) cc_final: 0.6337 (mp0) REVERT: Q 314 MET cc_start: 0.8477 (ttt) cc_final: 0.8086 (ttt) REVERT: S 403 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7204 (mt-10) REVERT: V 26 GLU cc_start: 0.6595 (mp0) cc_final: 0.6333 (mp0) REVERT: V 123 MET cc_start: 0.5698 (mmp) cc_final: 0.5482 (mmm) REVERT: X 314 MET cc_start: 0.8485 (ttt) cc_final: 0.8034 (ttt) outliers start: 32 outliers final: 8 residues processed: 543 average time/residue: 0.8945 time to fit residues: 578.4267 Evaluate side-chains 511 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 503 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain X residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 265 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 462 optimal weight: 20.0000 chunk 399 optimal weight: 9.9990 chunk 510 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 458 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 482 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN C 120 GLN C 151 GLN E 120 GLN E 151 GLN E 203 GLN G 203 GLN I 120 GLN I 151 GLN K 120 GLN K 151 GLN K 203 GLN M 151 GLN M 203 GLN O 120 GLN O 151 GLN Q 120 GLN Q 151 GLN Q 203 GLN S 151 GLN S 203 GLN V 120 GLN X 120 GLN X 151 GLN X 203 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.171202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.120762 restraints weight = 129849.345| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.61 r_work: 0.2787 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 43020 Z= 0.284 Angle : 0.716 11.288 58428 Z= 0.371 Chirality : 0.052 0.197 6696 Planarity : 0.005 0.042 7416 Dihedral : 5.199 23.377 5988 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.23 % Allowed : 8.73 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.11), residues: 5424 helix: 1.72 (0.13), residues: 1752 sheet: 0.50 (0.17), residues: 948 loop : -2.00 (0.10), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG V 110 TYR 0.016 0.002 TYR C 150 PHE 0.016 0.002 PHE A 183 TRP 0.011 0.002 TRP K 258 HIS 0.007 0.002 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00671 (42984) covalent geometry : angle 0.71586 (58428) hydrogen bonds : bond 0.04558 ( 1896) hydrogen bonds : angle 4.61970 ( 5268) metal coordination : bond 0.01184 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 504 time to evaluate : 1.659 Fit side-chains REVERT: A 54 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6325 (mm-30) REVERT: C 26 GLU cc_start: 0.6926 (mp0) cc_final: 0.6544 (mp0) REVERT: E 314 MET cc_start: 0.9028 (ttt) cc_final: 0.8826 (ttt) REVERT: G 54 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6317 (mm-30) REVERT: I 26 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7021 (mp0) REVERT: K 314 MET cc_start: 0.9029 (ttt) cc_final: 0.8800 (ttt) REVERT: O 26 GLU cc_start: 0.6967 (mp0) cc_final: 0.6600 (mp0) REVERT: S 54 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6318 (mm-30) REVERT: V 26 GLU cc_start: 0.6938 (mp0) cc_final: 0.6562 (mp0) REVERT: V 123 MET cc_start: 0.5054 (mmp) cc_final: 0.4764 (mmm) REVERT: X 314 MET cc_start: 0.9021 (ttt) cc_final: 0.8792 (ttt) outliers start: 43 outliers final: 21 residues processed: 541 average time/residue: 0.9075 time to fit residues: 585.9655 Evaluate side-chains 507 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 486 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 317 THR Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain V residue 317 THR Chi-restraints excluded: chain X residue 156 VAL Chi-restraints excluded: chain X residue 317 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 388 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 490 optimal weight: 20.0000 chunk 359 optimal weight: 6.9990 chunk 406 optimal weight: 0.6980 chunk 354 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 320 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN E 151 GLN G 151 GLN K 151 GLN M 151 GLN Q 151 GLN S 151 GLN V 151 GLN X 151 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.171203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.124056 restraints weight = 124843.211| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.51 r_work: 0.2765 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 43020 Z= 0.272 Angle : 0.705 7.452 58428 Z= 0.368 Chirality : 0.051 0.179 6696 Planarity : 0.005 0.039 7416 Dihedral : 5.279 23.414 5988 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.40 % Allowed : 9.34 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.11), residues: 5424 helix: 1.62 (0.13), residues: 1752 sheet: 0.55 (0.15), residues: 1140 loop : -2.06 (0.10), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 110 TYR 0.015 0.002 TYR C 150 PHE 0.017 0.002 PHE E 183 TRP 0.010 0.002 TRP I 258 HIS 0.007 0.002 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00641 (42984) covalent geometry : angle 0.70480 (58428) hydrogen bonds : bond 0.04470 ( 1896) hydrogen bonds : angle 4.63400 ( 5268) metal coordination : bond 0.01262 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 495 time to evaluate : 1.648 Fit side-chains REVERT: A 54 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6312 (mm-30) REVERT: A 403 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 26 GLU cc_start: 0.6989 (mp0) cc_final: 0.6616 (mp0) REVERT: C 123 MET cc_start: 0.5255 (mmp) cc_final: 0.4938 (mmm) REVERT: C 389 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: E 314 MET cc_start: 0.9036 (ttt) cc_final: 0.8797 (ttt) REVERT: E 448 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: G 54 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6305 (mm-30) REVERT: G 403 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7734 (mt-10) REVERT: I 26 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7059 (mp0) REVERT: I 123 MET cc_start: 0.5151 (mmp) cc_final: 0.4862 (mmm) REVERT: I 389 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: K 314 MET cc_start: 0.9039 (ttt) cc_final: 0.8807 (ttt) REVERT: K 448 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: M 403 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7735 (mt-10) REVERT: O 26 GLU cc_start: 0.6987 (mp0) cc_final: 0.6616 (mp0) REVERT: O 123 MET cc_start: 0.5170 (mmp) cc_final: 0.4858 (mmm) REVERT: O 389 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: Q 314 MET cc_start: 0.9054 (ttt) cc_final: 0.8758 (ttt) REVERT: Q 448 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: S 54 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6303 (mm-30) REVERT: S 403 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7758 (mt-10) REVERT: V 26 GLU cc_start: 0.6950 (mp0) cc_final: 0.6573 (mp0) REVERT: V 123 MET cc_start: 0.5250 (mmp) cc_final: 0.4923 (mmm) REVERT: V 389 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8412 (tm-30) REVERT: X 314 MET cc_start: 0.9033 (ttt) cc_final: 0.8800 (ttt) REVERT: X 448 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7976 (m-30) outliers start: 51 outliers final: 21 residues processed: 535 average time/residue: 0.9023 time to fit residues: 577.0955 Evaluate side-chains 519 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 490 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 448 ASP Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 317 THR Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 389 GLN Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain Q residue 317 THR Chi-restraints excluded: chain Q residue 448 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 317 THR Chi-restraints excluded: chain V residue 317 THR Chi-restraints excluded: chain V residue 389 GLN Chi-restraints excluded: chain X residue 156 VAL Chi-restraints excluded: chain X residue 317 THR Chi-restraints excluded: chain X residue 448 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 515 optimal weight: 3.9990 chunk 523 optimal weight: 0.9980 chunk 450 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 307 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 352 optimal weight: 0.7980 chunk 354 optimal weight: 8.9990 chunk 490 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN C 151 GLN E 151 GLN G 203 GLN I 151 GLN K 151 GLN M 203 GLN O 151 GLN Q 151 GLN S 151 GLN S 203 GLN X 151 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.176943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132400 restraints weight = 150821.307| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.71 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43020 Z= 0.130 Angle : 0.573 10.302 58428 Z= 0.298 Chirality : 0.044 0.145 6696 Planarity : 0.004 0.038 7416 Dihedral : 4.663 19.943 5988 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.69 % Allowed : 10.43 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.11), residues: 5424 helix: 1.91 (0.13), residues: 1812 sheet: 0.51 (0.15), residues: 1164 loop : -1.96 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 275 TYR 0.010 0.001 TYR O 150 PHE 0.013 0.001 PHE Q 183 TRP 0.006 0.001 TRP O 258 HIS 0.004 0.001 HIS Q 79 Details of bonding type rmsd covalent geometry : bond 0.00305 (42984) covalent geometry : angle 0.57286 (58428) hydrogen bonds : bond 0.03281 ( 1896) hydrogen bonds : angle 4.30880 ( 5268) metal coordination : bond 0.00484 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 505 time to evaluate : 1.664 Fit side-chains REVERT: A 15 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8632 (mt) REVERT: A 60 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.6940 (m) REVERT: A 403 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7125 (mt-10) REVERT: C 26 GLU cc_start: 0.6606 (mp0) cc_final: 0.6356 (mp0) REVERT: C 135 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7361 (mt) REVERT: E 314 MET cc_start: 0.8482 (ttt) cc_final: 0.8053 (ttt) REVERT: G 403 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7117 (mt-10) REVERT: I 26 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7079 (mp0) REVERT: M 403 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7127 (mt-10) REVERT: O 26 GLU cc_start: 0.6600 (mp0) cc_final: 0.6353 (mp0) REVERT: O 123 MET cc_start: 0.5827 (mmp) cc_final: 0.5626 (mmm) REVERT: Q 314 MET cc_start: 0.8500 (ttt) cc_final: 0.7970 (ttt) REVERT: S 403 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7140 (mt-10) REVERT: V 26 GLU cc_start: 0.6590 (mp0) cc_final: 0.6342 (mp0) outliers start: 19 outliers final: 4 residues processed: 520 average time/residue: 0.8827 time to fit residues: 550.1737 Evaluate side-chains 505 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 498 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain Q residue 156 VAL Chi-restraints excluded: chain X residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 40 optimal weight: 9.9990 chunk 375 optimal weight: 3.9990 chunk 108 optimal weight: 0.0170 chunk 248 optimal weight: 3.9990 chunk 52 optimal weight: 0.0370 chunk 282 optimal weight: 0.5980 chunk 442 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 534 optimal weight: 0.0370 chunk 499 optimal weight: 0.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN C 120 GLN C 151 GLN E 120 GLN E 203 GLN G 151 GLN I 120 GLN I 151 GLN K 120 GLN K 203 GLN M 151 GLN M 444 GLN O 120 GLN O 151 GLN Q 203 GLN S 151 GLN V 120 GLN X 120 GLN X 203 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.181133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132009 restraints weight = 146975.853| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.93 r_work: 0.2963 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 43020 Z= 0.098 Angle : 0.531 10.812 58428 Z= 0.274 Chirality : 0.042 0.145 6696 Planarity : 0.004 0.041 7416 Dihedral : 4.210 16.460 5988 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.33 % Allowed : 10.98 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.11), residues: 5424 helix: 2.32 (0.13), residues: 1800 sheet: 0.70 (0.15), residues: 1164 loop : -1.84 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 465 TYR 0.008 0.001 TYR V 150 PHE 0.012 0.001 PHE K 264 TRP 0.008 0.001 TRP O 199 HIS 0.004 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00227 (42984) covalent geometry : angle 0.53139 (58428) hydrogen bonds : bond 0.02698 ( 1896) hydrogen bonds : angle 4.13824 ( 5268) metal coordination : bond 0.00218 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 500 time to evaluate : 1.607 Fit side-chains REVERT: A 60 THR cc_start: 0.7090 (OUTLIER) cc_final: 0.6877 (m) REVERT: A 403 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 73 MET cc_start: 0.6158 (mmm) cc_final: 0.5754 (mmm) REVERT: C 400 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8151 (mttp) REVERT: C 402 MET cc_start: 0.8435 (mtm) cc_final: 0.8219 (ttm) REVERT: E 26 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6778 (mp0) REVERT: E 314 MET cc_start: 0.8893 (ttt) cc_final: 0.8529 (ttt) REVERT: I 73 MET cc_start: 0.6124 (mmm) cc_final: 0.5560 (mmm) REVERT: I 400 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8012 (mttp) REVERT: K 26 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6788 (mp0) REVERT: K 314 MET cc_start: 0.8882 (ttt) cc_final: 0.8400 (ttt) REVERT: M 403 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7590 (mt-10) REVERT: O 73 MET cc_start: 0.6105 (mmm) cc_final: 0.5730 (mmm) REVERT: O 123 MET cc_start: 0.5182 (mmp) cc_final: 0.4870 (mmm) REVERT: Q 26 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6786 (mp0) REVERT: V 400 LYS cc_start: 0.8482 (mmtm) cc_final: 0.8095 (mttp) REVERT: X 314 MET cc_start: 0.8892 (ttt) cc_final: 0.8404 (ttt) outliers start: 3 outliers final: 0 residues processed: 503 average time/residue: 0.8589 time to fit residues: 521.0376 Evaluate side-chains 462 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 461 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 360 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 375 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 454 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 451 optimal weight: 0.9990 chunk 66 optimal weight: 0.0170 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 151 GLN E 19 GLN G 19 GLN G 151 GLN K 19 GLN M 19 GLN M 151 GLN O 151 GLN Q 19 GLN S 19 GLN S 151 GLN X 19 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.178888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.139243 restraints weight = 141676.067| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.42 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43020 Z= 0.117 Angle : 0.542 8.686 58428 Z= 0.280 Chirality : 0.044 0.140 6696 Planarity : 0.004 0.040 7416 Dihedral : 4.337 23.623 5988 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.51 % Allowed : 10.76 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.12), residues: 5424 helix: 2.60 (0.13), residues: 1740 sheet: 0.75 (0.16), residues: 1164 loop : -1.79 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 275 TYR 0.011 0.001 TYR O 150 PHE 0.013 0.001 PHE K 183 TRP 0.008 0.001 TRP V 258 HIS 0.004 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00277 (42984) covalent geometry : angle 0.54212 (58428) hydrogen bonds : bond 0.03014 ( 1896) hydrogen bonds : angle 4.13919 ( 5268) metal coordination : bond 0.00267 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15115.93 seconds wall clock time: 259 minutes 23.83 seconds (15563.83 seconds total)