Starting phenix.real_space_refine (version: dev) on Mon Feb 27 10:17:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2023/7v2h_31645_updated.pdb" } resolution = 2.5 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 Process input model Symmetric amino acids flipped Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "I GLU 105": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M GLU 647": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 315": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "X GLU 123": "OE1" <-> "OE2" Residue "X GLU 143": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "b GLU 17": "OE1" <-> "OE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "e GLU 130": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "i GLU 269": "OE1" <-> "OE2" Residue "i GLU 318": "OE1" <-> "OE2" Residue "j TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 38": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 397": "OE1" <-> "OE2" Residue "m GLU 77": "OE1" <-> "OE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "m GLU 170": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o GLU 61": "OE1" <-> "OE2" Residue "p GLU 123": "OE1" <-> "OE2" Residue "p GLU 152": "OE1" <-> "OE2" Residue "r GLU 47": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s GLU 202": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "s GLU 227": "OE1" <-> "OE2" Residue "s GLU 253": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "w GLU 251": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 68293 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1161 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "X" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1005 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1277 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1028 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {' UQ': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'DCQ': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 337 Unusual residues: {'CDL': 2, 'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 139 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "j" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "k" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 343 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "m" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "n" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {' UQ': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.265 48.966 173.576 1.00 11.27 S ATOM 3060 SG CYS A 425 46.684 45.855 179.444 1.00 11.59 S ATOM 2738 SG CYS A 385 43.924 44.579 173.690 1.00 10.41 S ATOM 2699 SG CYS A 379 41.986 49.439 177.711 1.00 10.75 S ATOM 3961 SG CYS B 113 35.375 63.791 138.626 1.00 19.90 S ATOM 3980 SG CYS B 116 40.415 61.603 142.555 1.00 19.90 S ATOM 4003 SG CYS B 119 41.555 64.324 136.887 1.00 19.90 S ATOM 4332 SG CYS B 162 39.036 58.506 137.657 1.00 19.90 S ATOM 4030 SG CYS B 123 47.395 67.066 132.367 1.00 19.90 S ATOM 4256 SG CYS B 152 45.532 65.360 126.667 1.00 19.90 S ATOM 4303 SG CYS B 158 43.740 61.534 131.593 1.00 19.90 S ATOM 4282 SG CYS B 155 49.820 61.746 129.967 1.00 19.90 S ATOM 5724 SG CYS C 166 52.128 65.425 122.169 1.00 19.90 S ATOM 4996 SG CYS C 72 52.590 66.635 115.720 1.00 19.90 S ATOM 4990 SG CYS C 71 57.767 65.074 118.885 1.00 10.51 S ATOM 5494 SG CYS C 136 54.566 70.211 120.847 1.00 18.85 S ATOM 14949 SG CYS M 131 39.925 62.076 154.621 1.00 19.90 S ATOM 14928 SG CYS M 128 43.645 57.572 151.489 1.00 19.90 S ATOM 14989 SG CYS M 137 45.720 61.075 156.603 1.00 19.90 S ATOM 15321 SG CYS M 179 43.751 61.377 167.613 1.00 15.07 S ATOM 15675 SG CYS M 226 40.960 63.937 163.398 1.00 19.90 S ATOM 15345 SG CYS M 182 38.670 63.916 169.501 1.00 19.90 S ATOM 15298 SG CYS M 176 38.545 58.359 166.179 1.00 19.90 S ATOM 14546 SG CYS M 78 55.805 56.933 171.278 1.00 14.91 S ATOM 14647 SG CYS M 92 53.985 59.020 173.784 1.00 9.10 S ATOM 14435 SG CYS M 64 49.684 58.890 171.591 1.00 19.90 S ATOM 14521 SG CYS M 75 50.606 56.980 168.555 1.00 19.90 S ATOM 21484 SG CYS O 135 31.564 31.365 182.267 1.00 33.93 S ATOM 21518 SG CYS O 140 31.691 28.170 183.521 1.00 35.91 S ATOM 21798 SG CYS O 176 36.347 33.379 184.428 1.00 32.78 S ATOM 21821 SG CYS O 180 36.475 29.772 185.225 1.00 37.93 S ATOM 28560 SG CYS T 86 28.145 50.632 146.975 1.00 11.74 S ATOM 28738 SG CYS T 111 29.527 53.980 147.856 1.00 13.44 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 29.22, per 1000 atoms: 0.43 Number of scatterers: 68293 At special positions: 0 Unit cell: (213.766, 219.137, 229.879, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 482 16.00 P 49 15.00 Mg 1 11.99 O 12251 8.00 N 11238 7.00 C 44243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS h 43 " - pdb=" SG CYS h 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.04 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.68 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 150 " pdb="ZN ZN T 150 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 150 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 150 " - pdb=" SG CYS T 86 " 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15532 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 358 helices and 30 sheets defined 53.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.652A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.763A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.404A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 427 through 441 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 211 removed outlier: 5.709A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.131A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.122A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 39 removed outlier: 5.036A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 132 through 137 removed outlier: 3.739A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.033A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 78 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 60 through 62 No H-bonds generated for 'chain 'I' and resid 60 through 62' Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.042A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 3.520A pdb=" N MET J 92 " --> pdb=" O TYR J 89 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 141 through 145 Processing helix chain 'J' and resid 147 through 159 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 223 removed outlier: 4.350A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP J 222 " --> pdb=" O ALA J 218 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 254 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.860A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 348 No H-bonds generated for 'chain 'J' and resid 345 through 348' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.627A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.881A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 96 removed outlier: 4.396A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.931A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 160 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 3.734A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 138 through 146 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.626A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 396 Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 425 Processing helix chain 'M' and resid 449 through 457 removed outlier: 3.628A pdb=" N SER M 457 " --> pdb=" O ASP M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 486 through 503 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 557 through 559 No H-bonds generated for 'chain 'M' and resid 557 through 559' Processing helix chain 'M' and resid 577 through 579 No H-bonds generated for 'chain 'M' and resid 577 through 579' Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 654 Processing helix chain 'M' and resid 665 through 674 removed outlier: 3.970A pdb=" N LEU M 674 " --> pdb=" O GLU M 670 " (cutoff:3.500A) Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 702 No H-bonds generated for 'chain 'M' and resid 699 through 702' Processing helix chain 'M' and resid 705 through 715 Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.672A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 30 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.770A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.537A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix Processing helix chain 'O' and resid 95 through 104 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 209 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.558A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix removed outlier: 3.515A pdb=" N ASP P 102 " --> pdb=" O PHE P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.789A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 3.871A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 60 No H-bonds generated for 'chain 'Q' and resid 58 through 60' Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.833A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 139 Proline residue: Q 134 - end of helix removed outlier: 3.994A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.506A pdb=" N TRP Q 202 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.763A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.754A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 433 Processing helix chain 'Q' and resid 435 through 438 No H-bonds generated for 'chain 'Q' and resid 435 through 438' Processing helix chain 'Q' and resid 444 through 454 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 29 Proline residue: S 7 - end of helix Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 67 through 73 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 3 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 39 through 47 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 80 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 99 Proline residue: W 73 - end of helix removed outlier: 3.762A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 125 Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'W' and resid 139 through 142 No H-bonds generated for 'chain 'W' and resid 139 through 142' Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 137 removed outlier: 4.954A pdb=" N LYS X 137 " --> pdb=" O ILE X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 151 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.683A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Y' and resid 94 through 97 No H-bonds generated for 'chain 'Y' and resid 94 through 97' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.640A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.764A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.629A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 70 through 73 No H-bonds generated for 'chain 'b' and resid 70 through 73' Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'b' and resid 90 through 92 No H-bonds generated for 'chain 'b' and resid 90 through 92' Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 129 through 149 Processing helix chain 'd' and resid 29 through 57 removed outlier: 5.022A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 124 removed outlier: 3.870A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 174 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'e' and resid 99 through 107 Processing helix chain 'e' and resid 116 through 131 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 73 Processing helix chain 'g' and resid 18 through 22 Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.754A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 removed outlier: 4.037A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 88 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.715A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.218A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.924A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 146 through 148 No H-bonds generated for 'chain 'i' and resid 146 through 148' Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.967A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 193 removed outlier: 3.855A pdb=" N VAL i 193 " --> pdb=" O TRP i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.704A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN i 235 " --> pdb=" O SER i 231 " (cutoff:3.500A) Processing helix chain 'i' and resid 238 through 251 Processing helix chain 'i' and resid 258 through 273 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.577A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 31 through 34 No H-bonds generated for 'chain 'j' and resid 31 through 34' Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.561A pdb=" N LEU j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU j 64 " --> pdb=" O ILE j 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.528A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN j 80 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 51 Processing helix chain 'k' and resid 54 through 85 removed outlier: 3.887A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix Processing helix chain 'k' and resid 90 through 92 No H-bonds generated for 'chain 'k' and resid 90 through 92' Processing helix chain 'l' and resid 3 through 23 removed outlier: 3.620A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.731A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 28 Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.415A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.928A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 133 Processing helix chain 'l' and resid 137 through 155 Processing helix chain 'l' and resid 162 through 193 removed outlier: 3.986A pdb=" N GLY l 181 " --> pdb=" O ILE l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 198 through 204 Processing helix chain 'l' and resid 210 through 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 4.013A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 255 through 262 Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.016A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 4.532A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.107A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE l 335 " --> pdb=" O MET l 331 " (cutoff:3.500A) Processing helix chain 'l' and resid 356 through 358 No H-bonds generated for 'chain 'l' and resid 356 through 358' Processing helix chain 'l' and resid 367 through 380 Processing helix chain 'l' and resid 389 through 400 removed outlier: 4.624A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.702A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 470 removed outlier: 5.673A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE l 466 " --> pdb=" O ILE l 462 " (cutoff:3.500A) Processing helix chain 'l' and resid 484 through 487 No H-bonds generated for 'chain 'l' and resid 484 through 487' Processing helix chain 'l' and resid 489 through 509 removed outlier: 4.040A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.370A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 601 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 47 Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 108 Processing helix chain 'm' and resid 124 through 127 Processing helix chain 'm' and resid 138 through 147 removed outlier: 4.033A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 removed outlier: 3.516A pdb=" N ARG m 173 " --> pdb=" O MET m 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 34 removed outlier: 6.270A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix Processing helix chain 'o' and resid 20 through 23 Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.737A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 75 through 79 removed outlier: 3.753A pdb=" N ASN o 79 " --> pdb=" O ASN o 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 75 through 79' Processing helix chain 'o' and resid 84 through 117 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.520A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 4.804A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 16 Proline residue: r 7 - end of helix removed outlier: 4.150A pdb=" N LEU r 12 " --> pdb=" O THR r 8 " (cutoff:3.500A) Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.195A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 83 Proline residue: r 74 - end of helix removed outlier: 4.748A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS r 83 " --> pdb=" O ALA r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.861A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.585A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 140 through 171 removed outlier: 3.932A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 3.716A pdb=" N THR r 171 " --> pdb=" O GLN r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.886A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.086A pdb=" N LYS r 218 " --> pdb=" O LEU r 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 235 through 248 removed outlier: 3.639A pdb=" N GLY r 239 " --> pdb=" O LEU r 236 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR r 247 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR r 248 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 257 removed outlier: 3.637A pdb=" N MET r 257 " --> pdb=" O THR r 254 " (cutoff:3.500A) Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.673A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 removed outlier: 3.585A pdb=" N ILE r 286 " --> pdb=" O LEU r 282 " (cutoff:3.500A) Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.597A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.684A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix removed outlier: 3.706A pdb=" N THR r 448 " --> pdb=" O LEU r 444 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU r 449 " --> pdb=" O LEU r 445 " (cutoff:3.500A) Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.765A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 56 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.378A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.733A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.268A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 168 removed outlier: 3.516A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 192 removed outlier: 5.661A pdb=" N TRP s 179 " --> pdb=" O PHE s 176 " (cutoff:3.500A) Proline residue: s 180 - end of helix Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 removed outlier: 3.815A pdb=" N MET s 286 " --> pdb=" O TYR s 282 " (cutoff:3.500A) Processing helix chain 's' and resid 293 through 310 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 22 through 35 removed outlier: 4.946A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 80 through 91 Processing helix chain 'u' and resid 102 through 115 Processing helix chain 'v' and resid 3 through 9 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 81 through 124 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 50 through 52 No H-bonds generated for 'chain 'w' and resid 50 through 52' Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.692A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 3.505A pdb=" N PHE w 169 " --> pdb=" O ASP w 166 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.382A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 252 removed outlier: 5.346A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.850A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS w 252 " --> pdb=" O GLU w 248 " (cutoff:3.500A) Processing helix chain 'w' and resid 261 through 263 No H-bonds generated for 'chain 'w' and resid 261 through 263' Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.138A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 341 through 343 No H-bonds generated for 'chain 'w' and resid 341 through 343' Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 239 through 244 removed outlier: 6.381A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.045A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.607A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.496A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 228 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'M' and resid 196 through 198 Processing sheet with id= N, first strand: chain 'M' and resid 246 through 251 removed outlier: 3.563A pdb=" N ARG M 272 " --> pdb=" O SER M 264 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG M 266 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= P, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.659A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.320A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= S, first strand: chain 'N' and resid 60 through 63 removed outlier: 3.544A pdb=" N GLY N 40 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.463A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.671A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= W, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.501A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Y, first strand: chain 'T' and resid 77 through 79 Processing sheet with id= Z, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= AA, first strand: chain 'l' and resid 69 through 71 Processing sheet with id= AB, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.908A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.655A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'w' and resid 84 through 86 2951 hydrogen bonds defined for protein. 8118 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: 22.03 Time building geometry restraints manager: 24.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27762 1.40 - 1.62: 41278 1.62 - 1.85: 853 1.85 - 2.07: 4 2.07 - 2.29: 80 Bond restraints: 69977 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.260 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.632 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 69972 not shown) Histogram of bond angle deviations from ideal: 73.59 - 85.98: 76 85.98 - 98.37: 3 98.37 - 110.77: 23466 110.77 - 123.16: 67940 123.16 - 135.55: 3085 Bond angle restraints: 94570 Sorted by residual: angle pdb=" C LEU I 41 " pdb=" N PRO I 42 " pdb=" CA PRO I 42 " ideal model delta sigma weight residual 119.78 127.80 -8.02 1.03e+00 9.43e-01 6.06e+01 angle pdb=" C11 CDL V 201 " pdb=" CA5 CDL V 201 " pdb=" OA6 CDL V 201 " ideal model delta sigma weight residual 111.33 121.23 -9.90 1.32e+00 5.72e-01 5.61e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.92 -9.59 1.32e+00 5.72e-01 5.27e+01 angle pdb=" C11 CDL a 201 " pdb=" CA5 CDL a 201 " pdb=" OA6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.77 -9.44 1.32e+00 5.72e-01 5.10e+01 angle pdb=" C51 CDL V 201 " pdb=" CB5 CDL V 201 " pdb=" OB6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.65 -9.32 1.32e+00 5.72e-01 4.97e+01 ... (remaining 94565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 41021 35.09 - 70.19: 1155 70.19 - 105.28: 104 105.28 - 140.37: 16 140.37 - 175.47: 7 Dihedral angle restraints: 42303 sinusoidal: 18210 harmonic: 24093 Sorted by residual: dihedral pdb=" CA ARG P 44 " pdb=" C ARG P 44 " pdb=" N PRO P 45 " pdb=" CA PRO P 45 " ideal model delta harmonic sigma weight residual -180.00 -144.69 -35.31 0 5.00e+00 4.00e-02 4.99e+01 dihedral pdb=" CA LYS b 121 " pdb=" C LYS b 121 " pdb=" N GLU b 122 " pdb=" CA GLU b 122 " ideal model delta harmonic sigma weight residual 180.00 144.79 35.21 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 73.06 -175.47 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 42300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 9848 0.103 - 0.206: 320 0.206 - 0.309: 21 0.309 - 0.412: 4 0.412 - 0.515: 1 Chirality restraints: 10194 Sorted by residual: chirality pdb=" CA LEU I 41 " pdb=" N LEU I 41 " pdb=" C LEU I 41 " pdb=" CB LEU I 41 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CA THR M 180 " pdb=" N THR M 180 " pdb=" C THR M 180 " pdb=" CB THR M 180 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA PHE u 169 " pdb=" N PHE u 169 " pdb=" C PHE u 169 " pdb=" CB PHE u 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 10191 not shown) Planarity restraints: 11771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ J 402 " -0.550 2.00e-02 2.50e+03 4.70e-01 2.76e+03 pdb=" C23 UQ J 402 " 0.678 2.00e-02 2.50e+03 pdb=" C24 UQ J 402 " 0.416 2.00e-02 2.50e+03 pdb=" C25 UQ J 402 " -0.376 2.00e-02 2.50e+03 pdb=" C26 UQ J 402 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.358 2.00e-02 2.50e+03 3.29e-01 1.36e+03 pdb=" C18 UQ s 402 " -0.349 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.389 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.005 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " 0.308 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C13 UQ J 402 " -0.574 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.230 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " 0.050 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " -0.014 2.00e-02 2.50e+03 ... (remaining 11768 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 274 2.51 - 3.11: 48539 3.11 - 3.70: 107475 3.70 - 4.30: 164261 4.30 - 4.90: 264255 Nonbonded interactions: 584804 Sorted by model distance: nonbonded pdb=" N HIS G 103 " pdb=" OD2 ASP G 107 " model vdw 1.909 2.520 nonbonded pdb=" OH TYR w 118 " pdb=" O3' ADP w 401 " model vdw 2.063 2.440 nonbonded pdb=" OE1 GLU s 24 " pdb=" OH TYR s 228 " model vdw 2.101 2.440 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.115 2.440 nonbonded pdb=" OH TYR B 76 " pdb=" OE1 GLU Q 257 " model vdw 2.150 2.440 ... (remaining 584799 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 'G' and (resid 69 through 93 or (resid 94 through 97 and (name N or name \ CA or name C or name O or name CB )) or resid 98 through 101 or (resid 102 and ( \ name N or name CA or name C or name O or name CB )) or resid 103 through 156 or \ resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } 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: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 49 5.49 5 Mg 1 5.21 5 S 482 5.16 5 C 44243 2.51 5 N 11238 2.21 5 O 12251 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 10.910 Check model and map are aligned: 0.790 Process input model: 156.090 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.480 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 : 0.007 0.264 69977 Z= 0.458 Angle : 0.824 18.398 94570 Z= 0.431 Chirality : 0.045 0.515 10194 Planarity : 0.009 0.470 11771 Dihedral : 16.000 175.466 26744 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.20 (0.09), residues: 8173 helix: 1.67 (0.08), residues: 4342 sheet: 0.53 (0.25), residues: 431 loop : -0.26 (0.11), residues: 3400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1260 time to evaluate : 6.517 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 1264 average time/residue: 1.7745 time to fit residues: 2848.5269 Evaluate side-chains 1067 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1064 time to evaluate : 6.403 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 2 average time/residue: 0.5444 time to fit residues: 10.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 8.9990 chunk 610 optimal weight: 0.7980 chunk 338 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 411 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 630 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 383 optimal weight: 3.9990 chunk 469 optimal weight: 2.9990 chunk 731 optimal weight: 0.7980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 192 ASN E 45 ASN E 48 HIS F 76 ASN H 37 GLN I 13 ASN J 323 HIS L 86 ASN M 425 ASN M 663 ASN N 135 GLN Q 46 GLN Q 79 ASN U 40 ASN V 134 GLN X 142 GLN c 84 GLN g 18 ASN l 323 HIS l 603 ASN o 126 ASN p 13 GLN p 124 GLN r 43 ASN v 50 GLN w 235 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 69977 Z= 0.256 Angle : 0.605 13.857 94570 Z= 0.308 Chirality : 0.044 0.197 10194 Planarity : 0.005 0.062 11771 Dihedral : 13.999 176.219 10568 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.05 (0.09), residues: 8173 helix: 1.55 (0.08), residues: 4334 sheet: 0.47 (0.26), residues: 392 loop : -0.31 (0.10), residues: 3447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1080 time to evaluate : 6.565 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. outliers start: 121 outliers final: 56 residues processed: 1133 average time/residue: 1.7676 time to fit residues: 2562.5392 Evaluate side-chains 1101 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1045 time to evaluate : 6.289 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 32 residues processed: 26 average time/residue: 0.7668 time to fit residues: 40.9734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 608 optimal weight: 10.0000 chunk 497 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 732 optimal weight: 0.8980 chunk 791 optimal weight: 6.9990 chunk 652 optimal weight: 10.0000 chunk 726 optimal weight: 0.9990 chunk 249 optimal weight: 10.0000 chunk 587 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 45 ASN F 76 ASN H 37 GLN J 323 HIS M 425 ASN ** M 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN N 135 GLN Q 46 GLN T 43 GLN U 40 ASN V 134 GLN Y 54 GLN c 84 GLN c 115 ASN d 124 ASN g 18 ASN l 320 ASN o 126 ASN p 13 GLN p 124 GLN v 50 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 69977 Z= 0.148 Angle : 0.510 10.833 94570 Z= 0.261 Chirality : 0.040 0.207 10194 Planarity : 0.004 0.067 11771 Dihedral : 12.999 174.908 10568 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.15 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.22 (0.09), residues: 8173 helix: 1.69 (0.08), residues: 4344 sheet: 0.48 (0.25), residues: 400 loop : -0.24 (0.11), residues: 3429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1086 time to evaluate : 6.352 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 117 outliers final: 48 residues processed: 1143 average time/residue: 1.7724 time to fit residues: 2593.9961 Evaluate side-chains 1087 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1039 time to evaluate : 6.311 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 32 residues processed: 18 average time/residue: 0.8971 time to fit residues: 33.0702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.5980 chunk 550 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 349 optimal weight: 10.0000 chunk 491 optimal weight: 0.0060 chunk 734 optimal weight: 9.9990 chunk 778 optimal weight: 7.9990 chunk 383 optimal weight: 7.9990 chunk 696 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 overall best weight: 3.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS B 59 GLN E 45 ASN F 76 ASN H 37 GLN J 323 HIS ** M 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 663 ASN N 135 GLN O 153 GLN Q 46 GLN U 40 ASN V 134 GLN c 84 GLN g 18 ASN i 49 ASN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 34 ASN l 320 ASN o 126 ASN p 13 GLN p 124 GLN r 103 GLN r 304 GLN v 50 GLN w 239 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 69977 Z= 0.324 Angle : 0.634 13.259 94570 Z= 0.324 Chirality : 0.046 0.213 10194 Planarity : 0.005 0.063 11771 Dihedral : 12.986 172.978 10568 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.49 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 0.95 (0.09), residues: 8173 helix: 1.42 (0.08), residues: 4331 sheet: 0.41 (0.25), residues: 411 loop : -0.30 (0.10), residues: 3431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1051 time to evaluate : 6.574 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 143 outliers final: 76 residues processed: 1126 average time/residue: 1.7886 time to fit residues: 2582.6796 Evaluate side-chains 1107 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1031 time to evaluate : 6.341 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 48 residues processed: 29 average time/residue: 0.8560 time to fit residues: 47.3607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 3.9990 chunk 441 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 579 optimal weight: 0.5980 chunk 321 optimal weight: 9.9990 chunk 664 optimal weight: 8.9990 chunk 537 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 2.9990 chunk 698 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 45 ASN H 37 GLN I 13 ASN J 323 HIS M 334 GLN M 598 ASN M 663 ASN O 153 GLN O 246 GLN Q 46 GLN U 40 ASN V 134 GLN c 84 GLN g 18 ASN i 174 GLN l 320 ASN o 126 ASN p 13 GLN p 124 GLN w 132 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 69977 Z= 0.234 Angle : 0.572 11.635 94570 Z= 0.293 Chirality : 0.043 0.230 10194 Planarity : 0.005 0.065 11771 Dihedral : 12.631 173.477 10568 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.01 (0.09), residues: 8173 helix: 1.50 (0.08), residues: 4328 sheet: 0.47 (0.26), residues: 391 loop : -0.30 (0.10), residues: 3454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1051 time to evaluate : 6.524 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 73 residues processed: 1129 average time/residue: 1.7908 time to fit residues: 2606.7470 Evaluate side-chains 1113 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1040 time to evaluate : 6.553 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 50 residues processed: 25 average time/residue: 1.0536 time to fit residues: 48.1682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 5.9990 chunk 700 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 456 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 778 optimal weight: 5.9990 chunk 646 optimal weight: 10.0000 chunk 360 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 chunk 408 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 59 GLN E 45 ASN H 37 GLN J 323 HIS M 334 GLN M 598 ASN M 663 ASN N 135 GLN O 41 HIS O 246 GLN Q 46 GLN U 40 ASN V 134 GLN c 84 GLN d 124 ASN g 18 ASN l 320 ASN p 13 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 69977 Z= 0.403 Angle : 0.684 14.720 94570 Z= 0.350 Chirality : 0.049 0.224 10194 Planarity : 0.006 0.128 11771 Dihedral : 12.904 172.620 10568 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.27 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 0.69 (0.09), residues: 8173 helix: 1.20 (0.08), residues: 4336 sheet: 0.32 (0.25), residues: 411 loop : -0.41 (0.10), residues: 3426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1053 time to evaluate : 6.986 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 96 residues processed: 1135 average time/residue: 1.7844 time to fit residues: 2599.5821 Evaluate side-chains 1129 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1033 time to evaluate : 6.311 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 63 residues processed: 34 average time/residue: 1.0933 time to fit residues: 63.7044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 443 optimal weight: 8.9990 chunk 568 optimal weight: 1.9990 chunk 440 optimal weight: 0.9980 chunk 655 optimal weight: 10.0000 chunk 434 optimal weight: 9.9990 chunk 775 optimal weight: 10.0000 chunk 485 optimal weight: 2.9990 chunk 473 optimal weight: 0.6980 chunk 358 optimal weight: 0.2980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN H 37 GLN J 323 HIS M 334 GLN M 598 ASN M 663 ASN N 135 GLN O 41 HIS O 246 GLN ** P 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 GLN U 40 ASN V 134 GLN c 84 GLN g 18 ASN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 320 ASN p 13 GLN p 124 GLN r 138 ASN r 139 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 69977 Z= 0.180 Angle : 0.551 14.311 94570 Z= 0.282 Chirality : 0.041 0.246 10194 Planarity : 0.005 0.067 11771 Dihedral : 12.256 174.237 10568 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.86 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.03 (0.09), residues: 8173 helix: 1.53 (0.08), residues: 4324 sheet: 0.39 (0.25), residues: 397 loop : -0.31 (0.10), residues: 3452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1066 time to evaluate : 6.411 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 72 residues processed: 1149 average time/residue: 1.7711 time to fit residues: 2617.4431 Evaluate side-chains 1111 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1039 time to evaluate : 6.366 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 58 residues processed: 16 average time/residue: 0.6603 time to fit residues: 26.8938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 8.9990 chunk 309 optimal weight: 0.9980 chunk 463 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 493 optimal weight: 7.9990 chunk 528 optimal weight: 0.0570 chunk 383 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 609 optimal weight: 9.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN E 45 ASN H 37 GLN H 110 ASN J 323 HIS M 334 GLN M 598 ASN M 663 ASN N 135 GLN O 246 GLN Q 46 GLN U 40 ASN V 134 GLN c 84 GLN i 204 ASN l 320 ASN p 13 GLN p 124 GLN r 138 ASN r 139 GLN u 65 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 69977 Z= 0.218 Angle : 0.570 12.530 94570 Z= 0.290 Chirality : 0.043 0.234 10194 Planarity : 0.005 0.065 11771 Dihedral : 12.012 173.776 10568 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.57 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.05 (0.09), residues: 8173 helix: 1.54 (0.08), residues: 4325 sheet: 0.38 (0.25), residues: 399 loop : -0.28 (0.11), residues: 3449 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1051 time to evaluate : 6.516 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 76 residues processed: 1123 average time/residue: 1.8108 time to fit residues: 2621.6108 Evaluate side-chains 1118 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1042 time to evaluate : 6.391 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 58 residues processed: 20 average time/residue: 0.9107 time to fit residues: 36.8720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 1.9990 chunk 743 optimal weight: 0.8980 chunk 678 optimal weight: 2.9990 chunk 723 optimal weight: 5.9990 chunk 435 optimal weight: 5.9990 chunk 314 optimal weight: 0.8980 chunk 567 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 653 optimal weight: 8.9990 chunk 683 optimal weight: 3.9990 chunk 720 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN H 37 GLN J 323 HIS M 334 GLN M 598 ASN M 663 ASN N 135 GLN O 246 GLN Q 46 GLN U 40 ASN V 134 GLN c 84 GLN l 320 ASN p 13 GLN p 124 GLN u 65 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 69977 Z= 0.226 Angle : 0.576 12.183 94570 Z= 0.294 Chirality : 0.043 0.231 10194 Planarity : 0.005 0.065 11771 Dihedral : 11.869 173.789 10568 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.05 (0.09), residues: 8173 helix: 1.53 (0.08), residues: 4326 sheet: 0.39 (0.25), residues: 399 loop : -0.27 (0.11), residues: 3448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1045 time to evaluate : 6.482 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 66 residues processed: 1113 average time/residue: 1.8385 time to fit residues: 2633.3691 Evaluate side-chains 1105 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1039 time to evaluate : 6.402 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 58 residues processed: 10 average time/residue: 1.1283 time to fit residues: 24.8874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 4.9990 chunk 764 optimal weight: 5.9990 chunk 466 optimal weight: 2.9990 chunk 362 optimal weight: 7.9990 chunk 531 optimal weight: 2.9990 chunk 801 optimal weight: 3.9990 chunk 738 optimal weight: 0.9990 chunk 638 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 493 optimal weight: 6.9990 chunk 391 optimal weight: 0.0050 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS M 334 GLN M 598 ASN M 663 ASN N 135 GLN O 246 GLN Q 46 GLN U 40 ASN V 134 GLN c 84 GLN l 320 ASN p 13 GLN u 65 GLN v 50 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 69977 Z= 0.229 Angle : 0.579 12.064 94570 Z= 0.295 Chirality : 0.043 0.238 10194 Planarity : 0.005 0.064 11771 Dihedral : 11.739 173.760 10568 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.43 % Favored : 96.50 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.04 (0.09), residues: 8173 helix: 1.52 (0.08), residues: 4327 sheet: 0.38 (0.25), residues: 399 loop : -0.27 (0.11), residues: 3447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16346 Ramachandran restraints generated. 8173 Oldfield, 0 Emsley, 8173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1049 time to evaluate : 6.405 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 66 residues processed: 1115 average time/residue: 1.8080 time to fit residues: 2594.3854 Evaluate side-chains 1104 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1038 time to evaluate : 6.382 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 58 residues processed: 10 average time/residue: 0.8173 time to fit residues: 21.7490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 0.9980 chunk 680 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 588 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 639 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 656 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN E 45 ASN H 37 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS M 334 GLN M 425 ASN M 598 ASN M 663 ASN N 135 GLN O 246 GLN Q 46 GLN U 40 ASN V 134 GLN c 84 GLN l 320 ASN l 479 ASN p 124 GLN v 50 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103522 restraints weight = 78856.828| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.12 r_work: 0.2953 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 69977 Z= 0.196 Angle : 0.560 12.532 94570 Z= 0.285 Chirality : 0.042 0.237 10194 Planarity : 0.005 0.065 11771 Dihedral : 11.505 174.258 10568 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.66 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: 1.12 (0.09), residues: 8173 helix: 1.58 (0.08), residues: 4330 sheet: 0.43 (0.26), residues: 399 loop : -0.24 (0.11), residues: 3444 =============================================================================== Job complete usr+sys time: 34079.81 seconds wall clock time: 588 minutes 20.15 seconds (35300.15 seconds total)