Starting phenix.real_space_refine (version: dev) on Sat Apr 9 09:23:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0v_11024/04_2022/6z0v_11024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0v_11024/04_2022/6z0v_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0v_11024/04_2022/6z0v_11024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0v_11024/04_2022/6z0v_11024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0v_11024/04_2022/6z0v_11024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0v_11024/04_2022/6z0v_11024.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP: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: 41.60, per 1000 atoms: 0.97 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 - 3.50 Amino acid : False - 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: 16.69 Conformation dependent library (CDL) restraints added in 12.8 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 3.14 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: 20.77 Time building geometry restraints manager: 17.89 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: 99.30 - 106.27: 1300 106.27 - 113.24: 23521 113.24 - 120.21: 15353 120.21 - 127.18: 17740 127.18 - 134.16: 514 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 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 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 472 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.830 Check model and map are aligned: 0.590 Convert atoms to be neutral: 0.360 Process input model: 146.770 Find NCS groups from input model: 3.360 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:16.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 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 : 0.010 0.104 42984 Z= 0.635 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 0 poor density : 619 time to evaluate : 5.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 1.6423 time to fit residues: 1239.6198 Evaluate side-chains 493 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 5.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 20.0000 chunk 409 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 276 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 423 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 490 optimal weight: 20.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 C 429 HIS E 203 GLN E 389 GLN E 429 HIS G 203 GLN G 389 GLN I 111 ASN I 203 GLN I 429 HIS K 203 GLN K 389 GLN K 429 HIS M 203 GLN M 389 GLN O 111 ASN O 203 GLN O 429 HIS Q 203 GLN Q 429 HIS S 203 GLN S 389 GLN V 111 ASN V 203 GLN V 429 HIS X 203 GLN X 389 GLN X 429 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 42984 Z= 0.207 Angle : 0.593 8.199 58428 Z= 0.310 Chirality : 0.045 0.279 6696 Planarity : 0.004 0.036 7416 Dihedral : 5.073 20.062 5988 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.10), residues: 5424 helix: 0.51 (0.12), residues: 1752 sheet: 0.32 (0.15), residues: 1140 loop : -2.66 (0.09), residues: 2532 *********************** 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 574 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 547 time to evaluate : 4.934 Fit side-chains outliers start: 27 outliers final: 4 residues processed: 558 average time/residue: 1.7632 time to fit residues: 1185.9156 Evaluate side-chains 524 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 520 time to evaluate : 5.099 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 6.8717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 408 optimal weight: 3.9990 chunk 333 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 491 optimal weight: 1.9990 chunk 530 optimal weight: 3.9990 chunk 437 optimal weight: 10.0000 chunk 487 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 394 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 42984 Z= 0.258 Angle : 0.612 10.130 58428 Z= 0.316 Chirality : 0.046 0.252 6696 Planarity : 0.004 0.034 7416 Dihedral : 4.944 20.426 5988 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5424 helix: 1.27 (0.12), residues: 1752 sheet: 0.43 (0.15), residues: 1140 loop : -2.48 (0.09), residues: 2532 *********************** 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 529 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 510 time to evaluate : 5.418 Fit side-chains outliers start: 19 outliers final: 4 residues processed: 518 average time/residue: 1.6647 time to fit residues: 1057.8937 Evaluate side-chains 506 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 502 time to evaluate : 4.881 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 6.7677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 3.9990 chunk 369 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 329 optimal weight: 3.9990 chunk 493 optimal weight: 1.9990 chunk 521 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 chunk 467 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 42984 Z= 0.344 Angle : 0.659 6.902 58428 Z= 0.340 Chirality : 0.049 0.231 6696 Planarity : 0.005 0.032 7416 Dihedral : 5.141 21.963 5988 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 5424 helix: 1.41 (0.13), residues: 1752 sheet: 0.43 (0.15), residues: 1140 loop : -2.38 (0.10), residues: 2532 *********************** 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 542 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 504 time to evaluate : 4.827 Fit side-chains outliers start: 38 outliers final: 7 residues processed: 534 average time/residue: 1.6052 time to fit residues: 1050.0620 Evaluate side-chains 500 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 493 time to evaluate : 4.823 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.9379 time to fit residues: 8.9658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 8.9990 chunk 296 optimal weight: 0.0670 chunk 7 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 445 optimal weight: 20.0000 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 0.8980 chunk 468 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 overall best weight: 2.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 ASN ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 42984 Z= 0.290 Angle : 0.631 11.053 58428 Z= 0.324 Chirality : 0.046 0.139 6696 Planarity : 0.004 0.032 7416 Dihedral : 4.982 21.272 5988 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.11), residues: 5424 helix: 1.71 (0.13), residues: 1752 sheet: 0.30 (0.15), residues: 1164 loop : -2.27 (0.10), residues: 2508 *********************** 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 521 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 503 time to evaluate : 4.859 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 516 average time/residue: 1.6791 time to fit residues: 1054.0592 Evaluate side-chains 502 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 496 time to evaluate : 4.658 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.9318 time to fit residues: 8.9120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 30.0000 chunk 470 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 306 optimal weight: 0.0670 chunk 128 optimal weight: 3.9990 chunk 522 optimal weight: 6.9990 chunk 433 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 GLN ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 42984 Z= 0.191 Angle : 0.561 6.068 58428 Z= 0.289 Chirality : 0.043 0.142 6696 Planarity : 0.004 0.032 7416 Dihedral : 4.583 19.183 5988 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 5424 helix: 2.18 (0.13), residues: 1740 sheet: 0.39 (0.15), residues: 1164 loop : -2.15 (0.10), residues: 2520 *********************** 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 550 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 533 time to evaluate : 5.199 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 542 average time/residue: 1.5964 time to fit residues: 1062.3076 Evaluate side-chains 502 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 496 time to evaluate : 5.104 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 1.2238 time to fit residues: 9.9977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 439 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 520 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 GLN ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 151 GLN ** X 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 42984 Z= 0.366 Angle : 0.674 11.544 58428 Z= 0.347 Chirality : 0.049 0.154 6696 Planarity : 0.005 0.032 7416 Dihedral : 5.049 22.422 5988 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.11), residues: 5424 helix: 1.89 (0.13), residues: 1752 sheet: 0.39 (0.18), residues: 948 loop : -2.22 (0.09), residues: 2724 *********************** 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 525 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 505 time to evaluate : 5.083 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 519 average time/residue: 1.6498 time to fit residues: 1046.5844 Evaluate side-chains 502 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 493 time to evaluate : 4.614 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 1.9431 time to fit residues: 11.1769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 100 optimal weight: 0.0370 chunk 330 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 257 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 409 optimal weight: 2.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 42984 Z= 0.225 Angle : 0.591 7.709 58428 Z= 0.304 Chirality : 0.045 0.138 6696 Planarity : 0.004 0.032 7416 Dihedral : 4.758 24.609 5988 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5424 helix: 2.20 (0.13), residues: 1752 sheet: 0.37 (0.15), residues: 1164 loop : -2.14 (0.10), residues: 2508 *********************** 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 520 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 499 time to evaluate : 4.945 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 514 average time/residue: 1.6463 time to fit residues: 1033.8334 Evaluate side-chains 493 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 486 time to evaluate : 5.103 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 2.0512 time to fit residues: 9.5064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 4.9990 chunk 498 optimal weight: 0.9990 chunk 454 optimal weight: 1.9990 chunk 485 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 380 optimal weight: 0.0980 chunk 148 optimal weight: 20.0000 chunk 438 optimal weight: 5.9990 chunk 458 optimal weight: 8.9990 chunk 483 optimal weight: 0.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 151 GLN ** X 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 0.047 42984 Z= 0.220 Angle : 0.596 10.903 58428 Z= 0.305 Chirality : 0.044 0.156 6696 Planarity : 0.004 0.036 7416 Dihedral : 4.658 28.672 5988 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 5424 helix: 2.31 (0.13), residues: 1752 sheet: 0.46 (0.16), residues: 1044 loop : -2.07 (0.10), residues: 2628 *********************** 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 514 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 496 time to evaluate : 5.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 511 average time/residue: 1.6949 time to fit residues: 1054.1637 Evaluate side-chains 497 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 481 time to evaluate : 4.767 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 2.1635 time to fit residues: 11.5194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 0.7980 chunk 512 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 537 optimal weight: 6.9990 chunk 495 optimal weight: 10.0000 chunk 428 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 330 optimal weight: 9.9990 chunk 262 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 151 GLN Q 120 GLN ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 42984 Z= 0.169 Angle : 0.541 7.126 58428 Z= 0.279 Chirality : 0.043 0.140 6696 Planarity : 0.004 0.045 7416 Dihedral : 4.407 29.466 5988 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 5424 helix: 2.55 (0.13), residues: 1752 sheet: 0.52 (0.16), residues: 1164 loop : -1.99 (0.11), residues: 2508 ********************** 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 513 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 498 time to evaluate : 5.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 513 average time/residue: 1.7242 time to fit residues: 1084.1885 Evaluate side-chains 491 residues out of total 4632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 477 time to evaluate : 4.965 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 6.8010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 4.9990 chunk 456 optimal weight: 0.3980 chunk 131 optimal weight: 0.7980 chunk 395 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 119 optimal weight: 8.9990 chunk 429 optimal weight: 6.9990 chunk 179 optimal weight: 0.0970 chunk 440 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS E 151 GLN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 429 HIS ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 429 HIS ** Q 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 429 HIS ** X 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.178656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.133032 restraints weight = 151401.649| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.73 r_work: 0.3171 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 42984 Z= 0.161 Angle : 0.541 10.417 58428 Z= 0.276 Chirality : 0.042 0.160 6696 Planarity : 0.004 0.048 7416 Dihedral : 4.288 37.592 5988 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.12), residues: 5424 helix: 2.73 (0.13), residues: 1752 sheet: 0.65 (0.16), residues: 1164 loop : -1.94 (0.11), residues: 2508 =============================================================================== Job complete usr+sys time: 14630.45 seconds wall clock time: 263 minutes 16.28 seconds (15796.28 seconds total)