Starting phenix.real_space_refine on Sat Feb 17 05:50:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2024/7v2h_31645_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2024/7v2h_31645.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2024/7v2h_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_2024/7v2h_31645_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2024/7v2h_31645_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2024/7v2h_31645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2024/7v2h_31645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2024/7v2h_31645_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2h_31645/02_2024/7v2h_31645_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 25.85, per 1000 atoms: 0.38 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: 21.10 Conformation dependent library (CDL) restraints added in 8.8 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: 8.48 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: 22.19 Time building geometry restraints manager: 23.17 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: 41238 35.09 - 70.19: 1281 70.19 - 105.28: 120 105.28 - 140.37: 35 140.37 - 175.47: 9 Dihedral angle restraints: 42683 sinusoidal: 18590 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 42680 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 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.600 Check model and map are aligned: 0.750 Set scattering table: 0.460 Process input model: 155.640 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 16.842 175.466 27124 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 0.10 % Allowed : 0.22 % Favored : 99.68 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP W 48 HIS 0.007 0.001 HIS S 27 PHE 0.032 0.001 PHE Q 204 TYR 0.057 0.001 TYR C 142 ARG 0.007 0.000 ARG h 32 *********************** 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 : 5.813 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 REVERT: A 450 MET cc_start: 0.8785 (mtt) cc_final: 0.8421 (mtt) REVERT: F 75 LYS cc_start: 0.7875 (mttm) cc_final: 0.7539 (mtmp) REVERT: G 90 TYR cc_start: 0.8188 (t80) cc_final: 0.7778 (t80) REVERT: I 11 LEU cc_start: 0.7068 (tp) cc_final: 0.6860 (tp) REVERT: I 13 ASN cc_start: 0.7579 (m-40) cc_final: 0.7365 (m110) REVERT: U 47 ARG cc_start: 0.8390 (mtt-85) cc_final: 0.7917 (ttp-110) REVERT: a 71 MET cc_start: 0.8908 (ttp) cc_final: 0.8625 (ttm) REVERT: c 150 TYR cc_start: 0.7417 (m-10) cc_final: 0.7217 (m-80) REVERT: c 160 GLN cc_start: 0.8494 (mt0) cc_final: 0.8112 (mt0) REVERT: c 165 ASP cc_start: 0.7751 (t70) cc_final: 0.7382 (t70) REVERT: f 73 ASN cc_start: 0.8281 (m-40) cc_final: 0.8019 (m110) REVERT: g 47 ASP cc_start: 0.8711 (t0) cc_final: 0.8387 (t0) REVERT: i 68 MET cc_start: 0.8931 (mmp) cc_final: 0.8728 (mmp) REVERT: i 245 MET cc_start: 0.8605 (tmm) cc_final: 0.8215 (tmm) REVERT: l 482 MET cc_start: 0.8487 (ptp) cc_final: 0.8228 (ptp) REVERT: n 46 LYS cc_start: 0.7889 (tttp) cc_final: 0.7496 (tptm) REVERT: p 51 HIS cc_start: 0.8211 (m-70) cc_final: 0.8000 (m-70) REVERT: p 106 ASP cc_start: 0.8522 (m-30) cc_final: 0.8180 (m-30) REVERT: r 229 MET cc_start: 0.9267 (mtp) cc_final: 0.8821 (mtp) REVERT: s 85 MET cc_start: 0.8778 (mmm) cc_final: 0.8575 (mmm) REVERT: s 202 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7283 (tt0) outliers start: 7 outliers final: 3 residues processed: 1264 average time/residue: 1.7345 time to fit residues: 2765.4854 Evaluate side-chains 1068 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1064 time to evaluate : 5.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain s residue 202 GLU 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 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0911 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 : 0.600 14.338 94570 Z= 0.305 Chirality : 0.044 0.198 10194 Planarity : 0.005 0.062 11771 Dihedral : 15.957 177.052 10957 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 1.65 % Allowed : 7.58 % Favored : 90.77 % 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: 1.07 (0.09), residues: 8173 helix: 1.56 (0.08), residues: 4336 sheet: 0.43 (0.25), residues: 409 loop : -0.29 (0.11), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.012 0.001 HIS S 27 PHE 0.032 0.002 PHE i 292 TYR 0.049 0.002 TYR C 142 ARG 0.008 0.000 ARG M 246 *********************** 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 1195 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1077 time to evaluate : 6.069 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: A 52 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7564 (mtm-85) REVERT: A 450 MET cc_start: 0.8784 (mtt) cc_final: 0.8399 (mtt) REVERT: E 69 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8279 (ttpm) REVERT: F 75 LYS cc_start: 0.8005 (mttm) cc_final: 0.7620 (mtmp) REVERT: G 105 MET cc_start: 0.7089 (mpp) cc_final: 0.6705 (mmt) REVERT: I 11 LEU cc_start: 0.7136 (tp) cc_final: 0.6910 (tp) REVERT: I 13 ASN cc_start: 0.7684 (m-40) cc_final: 0.7442 (m110) REVERT: L 148 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: L 154 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8342 (ptpt) REVERT: M 441 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6946 (ttp-170) REVERT: Q 194 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8194 (mt) REVERT: Q 203 MET cc_start: 0.8716 (mmm) cc_final: 0.8097 (mmm) REVERT: T 43 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8599 (tm-30) REVERT: T 47 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6883 (p0) REVERT: T 78 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: U 41 TYR cc_start: 0.8625 (m-80) cc_final: 0.8305 (m-10) REVERT: X 142 GLN cc_start: 0.8435 (tp40) cc_final: 0.8147 (tp40) REVERT: Z 14 MET cc_start: 0.4845 (OUTLIER) cc_final: 0.4400 (ppp) REVERT: a 71 MET cc_start: 0.8983 (ttp) cc_final: 0.8673 (ttm) REVERT: a 97 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: a 153 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: b 85 TYR cc_start: 0.9179 (t80) cc_final: 0.8698 (t80) REVERT: c 150 TYR cc_start: 0.7646 (m-10) cc_final: 0.7274 (m-80) REVERT: c 165 ASP cc_start: 0.7684 (t70) cc_final: 0.7360 (t70) REVERT: d 15 ARG cc_start: 0.6965 (ptm160) cc_final: 0.6419 (ttm-80) REVERT: h 37 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: h 39 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8493 (mm-30) REVERT: i 1 MET cc_start: 0.8778 (ttm) cc_final: 0.8485 (ttm) REVERT: i 245 MET cc_start: 0.8671 (tmm) cc_final: 0.8240 (tmm) REVERT: j 68 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: l 410 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7659 (tp) REVERT: n 30 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6893 (mmt90) REVERT: n 46 LYS cc_start: 0.7832 (tttp) cc_final: 0.7481 (tptm) REVERT: p 106 ASP cc_start: 0.8514 (m-30) cc_final: 0.8124 (m-30) REVERT: r 3 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8068 (ptpp) REVERT: r 19 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7846 (mttp) REVERT: r 229 MET cc_start: 0.9262 (mtp) cc_final: 0.8891 (mtp) REVERT: s 70 MET cc_start: 0.8026 (mtp) cc_final: 0.7800 (mtm) REVERT: s 85 MET cc_start: 0.8833 (mmm) cc_final: 0.8565 (mmm) REVERT: u 64 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8660 (m110) REVERT: v 70 LYS cc_start: 0.8349 (mmtp) cc_final: 0.8132 (mmtm) REVERT: v 88 ASP cc_start: 0.8328 (m-30) cc_final: 0.8127 (m-30) REVERT: w 272 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7159 (m-30) outliers start: 118 outliers final: 53 residues processed: 1128 average time/residue: 1.7214 time to fit residues: 2456.4030 Evaluate side-chains 1108 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1036 time to evaluate : 5.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 153 GLU Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 278 MET Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain p residue 44 MET Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 3 LYS Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 375 LEU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 272 ASP 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: 0.5980 chunk 497 optimal weight: 3.9990 chunk 201 optimal weight: 0.2980 chunk 732 optimal weight: 0.9980 chunk 791 optimal weight: 5.9990 chunk 652 optimal weight: 9.9990 chunk 726 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 587 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 M 666 GLN N 135 GLN Q 46 GLN U 40 ASN V 134 GLN Y 54 GLN c 84 GLN c 115 ASN d 124 ASN f 73 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 69977 Z= 0.170 Angle : 0.524 11.032 94570 Z= 0.268 Chirality : 0.041 0.207 10194 Planarity : 0.004 0.066 11771 Dihedral : 14.814 174.556 10954 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 1.78 % Allowed : 8.98 % Favored : 89.24 % 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: 1.18 (0.09), residues: 8173 helix: 1.65 (0.08), residues: 4342 sheet: 0.46 (0.25), residues: 400 loop : -0.26 (0.11), residues: 3431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.030 0.001 PHE i 292 TYR 0.024 0.001 TYR C 142 ARG 0.009 0.000 ARG p 65 *********************** 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 1216 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1089 time to evaluate : 5.913 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 450 MET cc_start: 0.8760 (mtt) cc_final: 0.8433 (mtt) REVERT: F 75 LYS cc_start: 0.8006 (mttm) cc_final: 0.7648 (mtmp) REVERT: G 90 TYR cc_start: 0.8215 (t80) cc_final: 0.7861 (t80) REVERT: G 105 MET cc_start: 0.7133 (mpp) cc_final: 0.6765 (mmt) REVERT: I 11 LEU cc_start: 0.7099 (tp) cc_final: 0.6884 (tp) REVERT: I 13 ASN cc_start: 0.7578 (m-40) cc_final: 0.7355 (m110) REVERT: L 148 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: M 441 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6999 (ttp-170) REVERT: N 67 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7656 (tm-30) REVERT: Q 57 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: Q 194 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8140 (mt) REVERT: Q 203 MET cc_start: 0.8652 (mmm) cc_final: 0.8074 (mmm) REVERT: T 47 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6861 (p0) REVERT: T 78 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: U 41 TYR cc_start: 0.8631 (m-80) cc_final: 0.8285 (m-10) REVERT: X 142 GLN cc_start: 0.8499 (tp40) cc_final: 0.8181 (tp40) REVERT: Z 14 MET cc_start: 0.4940 (OUTLIER) cc_final: 0.4453 (ppp) REVERT: a 71 MET cc_start: 0.8921 (ttp) cc_final: 0.8677 (ttm) REVERT: a 153 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: b 85 TYR cc_start: 0.9170 (t80) cc_final: 0.8676 (t80) REVERT: b 117 ILE cc_start: 0.8581 (mm) cc_final: 0.8371 (mp) REVERT: c 150 TYR cc_start: 0.7436 (m-10) cc_final: 0.7110 (m-80) REVERT: c 160 GLN cc_start: 0.8390 (mt0) cc_final: 0.7934 (mt0) REVERT: c 165 ASP cc_start: 0.7625 (t70) cc_final: 0.7125 (t70) REVERT: h 39 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8487 (mm-30) REVERT: i 245 MET cc_start: 0.8682 (tmm) cc_final: 0.8298 (tmm) REVERT: i 270 MET cc_start: 0.8563 (mtp) cc_final: 0.8044 (mtp) REVERT: j 68 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: l 410 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7698 (tp) REVERT: n 46 LYS cc_start: 0.7779 (tttp) cc_final: 0.7453 (tptm) REVERT: o 30 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7811 (mmt180) REVERT: p 106 ASP cc_start: 0.8615 (m-30) cc_final: 0.8166 (m-30) REVERT: r 204 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8644 (mmt) REVERT: r 229 MET cc_start: 0.9218 (mtp) cc_final: 0.8791 (mtp) REVERT: r 257 MET cc_start: 0.9008 (mmm) cc_final: 0.8627 (mmm) REVERT: r 378 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: u 64 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8588 (m110) REVERT: v 52 MET cc_start: 0.6934 (mmm) cc_final: 0.6379 (mpp) REVERT: v 70 LYS cc_start: 0.8253 (mmtp) cc_final: 0.8021 (mmtm) REVERT: v 88 ASP cc_start: 0.8337 (m-30) cc_final: 0.8096 (m-30) outliers start: 127 outliers final: 54 residues processed: 1146 average time/residue: 1.7086 time to fit residues: 2482.0962 Evaluate side-chains 1113 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1045 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 365 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain M residue 55 LYS Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 153 GLU Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 204 MET Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 2.9990 chunk 550 optimal weight: 10.0000 chunk 380 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 349 optimal weight: 5.9990 chunk 491 optimal weight: 0.6980 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: 3.0586 ------------------------------------------------------------------------------- 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 T 43 GLN U 40 ASN V 134 GLN c 84 GLN g 18 ASN i 49 ASN i 174 GLN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 320 ASN o 126 ASN p 13 GLN p 124 GLN r 103 GLN r 304 GLN v 50 GLN w 132 GLN w 239 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 69977 Z= 0.293 Angle : 0.613 12.728 94570 Z= 0.314 Chirality : 0.045 0.212 10194 Planarity : 0.005 0.063 11771 Dihedral : 14.621 173.114 10954 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 2.08 % Allowed : 10.03 % Favored : 87.89 % 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: 0.99 (0.09), residues: 8173 helix: 1.47 (0.08), residues: 4326 sheet: 0.45 (0.25), residues: 393 loop : -0.31 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP u 86 HIS 0.010 0.001 HIS P 196 PHE 0.030 0.002 PHE i 292 TYR 0.021 0.002 TYR o 77 ARG 0.010 0.001 ARG p 65 *********************** 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 1201 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1052 time to evaluate : 5.833 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 450 MET cc_start: 0.8746 (mtt) cc_final: 0.8318 (mtt) REVERT: C 79 MET cc_start: 0.9246 (ttp) cc_final: 0.8981 (ttp) REVERT: G 105 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6690 (mmt) REVERT: I 11 LEU cc_start: 0.7154 (tp) cc_final: 0.6910 (tp) REVERT: K 106 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: L 148 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: L 154 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8133 (ptpt) REVERT: M 204 MET cc_start: 0.9045 (ttp) cc_final: 0.8804 (ttm) REVERT: M 441 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7037 (ttp-170) REVERT: N 67 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7614 (tm-30) REVERT: Q 57 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6093 (pm20) REVERT: Q 99 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8150 (mtm) REVERT: Q 194 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8225 (mt) REVERT: S 28 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8472 (mtpt) REVERT: T 47 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6922 (p0) REVERT: T 78 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: U 41 TYR cc_start: 0.8651 (m-80) cc_final: 0.8268 (m-10) REVERT: X 142 GLN cc_start: 0.8499 (tp40) cc_final: 0.8168 (tp40) REVERT: Y 41 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: Z 14 MET cc_start: 0.5014 (OUTLIER) cc_final: 0.4494 (ppp) REVERT: a 71 MET cc_start: 0.8951 (ttp) cc_final: 0.8667 (ttm) REVERT: a 97 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: a 153 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: b 85 TYR cc_start: 0.9201 (t80) cc_final: 0.8725 (t80) REVERT: c 150 TYR cc_start: 0.7673 (m-10) cc_final: 0.7199 (m-80) REVERT: c 165 ASP cc_start: 0.7642 (t70) cc_final: 0.7242 (t70) REVERT: h 37 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: h 39 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8352 (mm-30) REVERT: h 73 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7859 (mmm) REVERT: h 85 LYS cc_start: 0.7728 (tttt) cc_final: 0.7362 (tttp) REVERT: i 245 MET cc_start: 0.8717 (tmm) cc_final: 0.8404 (tmm) REVERT: i 270 MET cc_start: 0.8592 (mtp) cc_final: 0.8100 (mtp) REVERT: j 68 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: n 30 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6982 (mmm160) REVERT: p 55 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.6705 (tptp) REVERT: p 106 ASP cc_start: 0.8674 (m-30) cc_final: 0.8219 (m-30) REVERT: r 3 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8078 (ptpp) REVERT: r 19 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7898 (mttp) REVERT: r 378 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: s 24 GLU cc_start: 0.8490 (tt0) cc_final: 0.8208 (tt0) REVERT: u 64 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8628 (m110) REVERT: v 52 MET cc_start: 0.6891 (mmm) cc_final: 0.6564 (mpp) REVERT: v 88 ASP cc_start: 0.8378 (m-30) cc_final: 0.8150 (m-30) outliers start: 149 outliers final: 77 residues processed: 1129 average time/residue: 1.7236 time to fit residues: 2466.0448 Evaluate side-chains 1132 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1032 time to evaluate : 5.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 365 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 140 LYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 153 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 127 ARG Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 3 LYS Chi-restraints excluded: chain r residue 19 LYS Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 378 GLU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 4.9990 chunk 441 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 579 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 664 optimal weight: 8.9990 chunk 537 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 698 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 153 GLN O 246 GLN Q 46 GLN U 40 ASN V 134 GLN c 84 GLN d 134 GLN g 18 ASN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 320 ASN o 126 ASN p 13 GLN p 124 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 69977 Z= 0.407 Angle : 0.688 14.378 94570 Z= 0.353 Chirality : 0.049 0.259 10194 Planarity : 0.006 0.072 11771 Dihedral : 14.756 173.806 10952 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 2.49 % Allowed : 10.39 % Favored : 87.12 % 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: 0.67 (0.09), residues: 8173 helix: 1.18 (0.08), residues: 4335 sheet: 0.32 (0.25), residues: 406 loop : -0.43 (0.10), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP u 86 HIS 0.011 0.002 HIS P 196 PHE 0.032 0.003 PHE i 292 TYR 0.024 0.003 TYR Y 44 ARG 0.011 0.001 ARG p 65 *********************** 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 1228 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1050 time to evaluate : 5.883 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7547 (mtm-85) REVERT: A 224 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8027 (mtm180) REVERT: F 40 ARG cc_start: 0.7331 (mtt180) cc_final: 0.7066 (mtt180) REVERT: G 105 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6646 (mmt) REVERT: I 11 LEU cc_start: 0.7149 (tp) cc_final: 0.6888 (tp) REVERT: K 106 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: L 148 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: L 154 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8062 (ptpt) REVERT: M 77 MET cc_start: 0.9221 (tpt) cc_final: 0.8766 (tpp) REVERT: Q 57 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: Q 99 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8192 (mtm) REVERT: Q 194 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8262 (mt) REVERT: S 28 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8517 (mtpt) REVERT: T 47 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6881 (p0) REVERT: T 78 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: U 41 TYR cc_start: 0.8695 (m-80) cc_final: 0.8308 (m-10) REVERT: X 142 GLN cc_start: 0.8563 (tp40) cc_final: 0.8246 (tp40) REVERT: Y 41 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: Z 49 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: a 71 MET cc_start: 0.8944 (ttp) cc_final: 0.8669 (ttm) REVERT: a 97 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7073 (pt0) REVERT: a 160 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8786 (mtt) REVERT: b 85 TYR cc_start: 0.9196 (t80) cc_final: 0.8711 (t80) REVERT: c 74 ASP cc_start: 0.7707 (t0) cc_final: 0.7469 (t0) REVERT: c 140 MET cc_start: 0.8776 (mmm) cc_final: 0.8546 (mmm) REVERT: c 150 TYR cc_start: 0.7835 (m-10) cc_final: 0.7437 (m-80) REVERT: c 160 GLN cc_start: 0.8419 (mt0) cc_final: 0.8010 (mt0) REVERT: c 165 ASP cc_start: 0.7643 (t70) cc_final: 0.7251 (t70) REVERT: h 37 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: h 39 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8371 (mm-30) REVERT: h 85 LYS cc_start: 0.7763 (tttt) cc_final: 0.7365 (tttp) REVERT: i 245 MET cc_start: 0.8714 (tmm) cc_final: 0.8455 (tmm) REVERT: j 68 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: l 383 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7170 (tpp) REVERT: n 30 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6990 (mmm160) REVERT: n 46 LYS cc_start: 0.7947 (tttp) cc_final: 0.7734 (tptm) REVERT: o 30 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7450 (mmt180) REVERT: p 55 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.6697 (tptp) REVERT: p 106 ASP cc_start: 0.8702 (m-30) cc_final: 0.8178 (m-30) REVERT: r 3 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8068 (ptpp) REVERT: u 17 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: u 64 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8628 (m110) REVERT: v 88 ASP cc_start: 0.8420 (m-30) cc_final: 0.8203 (m-30) outliers start: 178 outliers final: 96 residues processed: 1144 average time/residue: 1.7135 time to fit residues: 2488.3877 Evaluate side-chains 1154 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1034 time to evaluate : 5.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 117 ARG Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 365 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 106 GLN Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 107 LYS Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 55 LEU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 182 SER Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 63 ASP Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 261 MET Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 387 THR Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 127 ARG Chi-restraints excluded: chain p residue 151 THR Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 3 LYS Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain s residue 13 ILE Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 4.9990 chunk 700 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 456 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 778 optimal weight: 4.9990 chunk 646 optimal weight: 7.9990 chunk 360 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 408 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 J 323 HIS 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 u 65 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 69977 Z= 0.161 Angle : 0.525 10.831 94570 Z= 0.269 Chirality : 0.041 0.237 10194 Planarity : 0.004 0.068 11771 Dihedral : 13.842 174.585 10952 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 1.73 % Allowed : 11.66 % Favored : 86.60 % 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: 1.10 (0.09), residues: 8173 helix: 1.59 (0.08), residues: 4327 sheet: 0.44 (0.26), residues: 397 loop : -0.28 (0.10), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.031 0.001 PHE i 292 TYR 0.021 0.001 TYR l 422 ARG 0.011 0.000 ARG p 65 *********************** 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 1211 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1087 time to evaluate : 6.031 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 REVERT: C 79 MET cc_start: 0.9177 (ttp) cc_final: 0.8834 (ttp) REVERT: G 105 MET cc_start: 0.7016 (mpp) cc_final: 0.6632 (mmt) REVERT: I 11 LEU cc_start: 0.7101 (tp) cc_final: 0.6855 (tp) REVERT: L 148 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: N 67 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7478 (tm-30) REVERT: Q 57 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6126 (pm20) REVERT: Q 99 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8163 (mtm) REVERT: Q 194 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8164 (mt) REVERT: T 47 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6829 (p0) REVERT: U 41 TYR cc_start: 0.8618 (m-80) cc_final: 0.8337 (m-10) REVERT: X 82 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7909 (mtt180) REVERT: X 142 GLN cc_start: 0.8522 (tp40) cc_final: 0.8264 (tp40) REVERT: Y 41 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: a 153 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: b 85 TYR cc_start: 0.9200 (t80) cc_final: 0.8687 (t80) REVERT: c 150 TYR cc_start: 0.7482 (m-10) cc_final: 0.7111 (m-80) REVERT: c 160 GLN cc_start: 0.8372 (mt0) cc_final: 0.8031 (mt0) REVERT: c 165 ASP cc_start: 0.7630 (t70) cc_final: 0.7092 (t70) REVERT: d 78 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6304 (mt-10) REVERT: f 68 GLU cc_start: 0.7927 (tp30) cc_final: 0.7631 (tp30) REVERT: g 47 ASP cc_start: 0.8694 (t0) cc_final: 0.8289 (t70) REVERT: h 39 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8477 (mm-30) REVERT: h 73 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7792 (mmm) REVERT: h 85 LYS cc_start: 0.7723 (tttt) cc_final: 0.7341 (tttp) REVERT: i 187 MET cc_start: 0.8657 (mmp) cc_final: 0.8173 (mmp) REVERT: i 245 MET cc_start: 0.8646 (tmm) cc_final: 0.8230 (tmm) REVERT: j 68 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: l 59 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7666 (tp40) REVERT: n 30 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6562 (mmm160) REVERT: n 46 LYS cc_start: 0.7782 (tttp) cc_final: 0.7502 (tptm) REVERT: p 55 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.6638 (tptp) REVERT: p 65 ARG cc_start: 0.7698 (mtp-110) cc_final: 0.7144 (mtm180) REVERT: p 106 ASP cc_start: 0.8626 (m-30) cc_final: 0.8105 (m-30) REVERT: r 204 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8542 (mmt) REVERT: u 64 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8619 (m110) REVERT: v 88 ASP cc_start: 0.8367 (m-30) cc_final: 0.8121 (m-30) outliers start: 124 outliers final: 55 residues processed: 1149 average time/residue: 1.7266 time to fit residues: 2518.1901 Evaluate side-chains 1119 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1048 time to evaluate : 5.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 365 GLU Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain X residue 82 ARG Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 153 GLU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain l residue 59 GLN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 496 MET Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 204 MET Chi-restraints excluded: chain s residue 31 MET Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 443 optimal weight: 6.9990 chunk 568 optimal weight: 0.2980 chunk 440 optimal weight: 7.9990 chunk 655 optimal weight: 10.0000 chunk 434 optimal weight: 10.0000 chunk 775 optimal weight: 10.0000 chunk 485 optimal weight: 7.9990 chunk 473 optimal weight: 9.9990 chunk 358 optimal weight: 0.8980 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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 F 76 ASN H 37 GLN H 110 ASN J 323 HIS M 334 GLN M 598 ASN M 663 ASN M 666 GLN 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 w 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1366 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= 0.247 Angle : 0.579 14.389 94570 Z= 0.295 Chirality : 0.043 0.261 10194 Planarity : 0.005 0.065 11771 Dihedral : 13.789 173.519 10950 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 1.80 % Allowed : 11.99 % Favored : 86.21 % 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: 1.06 (0.09), residues: 8173 helix: 1.54 (0.08), residues: 4327 sheet: 0.41 (0.26), residues: 397 loop : -0.27 (0.11), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.008 0.001 HIS P 196 PHE 0.030 0.002 PHE i 292 TYR 0.025 0.002 TYR b 88 ARG 0.009 0.000 ARG p 65 *********************** 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: 129 poor density : 1056 time to evaluate : 6.037 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: G 105 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6689 (mmt) REVERT: I 11 LEU cc_start: 0.7119 (tp) cc_final: 0.6870 (tp) REVERT: L 148 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: N 67 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7546 (tm-30) REVERT: Q 57 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6201 (pm20) REVERT: Q 99 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8170 (mtm) REVERT: Q 194 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8208 (mt) REVERT: Q 258 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8838 (tt) REVERT: S 28 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8050 (mtmt) REVERT: T 47 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6838 (p0) REVERT: U 41 TYR cc_start: 0.8614 (m-80) cc_final: 0.8317 (m-10) REVERT: X 142 GLN cc_start: 0.8560 (tp40) cc_final: 0.8231 (tp40) REVERT: Y 41 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7265 (mm-30) REVERT: Z 49 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: a 97 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: a 160 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8785 (mtt) REVERT: b 85 TYR cc_start: 0.9219 (t80) cc_final: 0.8719 (t80) REVERT: c 150 TYR cc_start: 0.7601 (m-10) cc_final: 0.7268 (m-80) REVERT: c 160 GLN cc_start: 0.8364 (mt0) cc_final: 0.8006 (mt0) REVERT: c 165 ASP cc_start: 0.7649 (t70) cc_final: 0.7127 (t70) REVERT: d 78 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6260 (mt-10) REVERT: f 68 GLU cc_start: 0.7945 (tp30) cc_final: 0.7624 (tp30) REVERT: h 39 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8400 (mm-30) REVERT: h 73 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7798 (mmm) REVERT: h 85 LYS cc_start: 0.7739 (tttt) cc_final: 0.7353 (tttp) REVERT: i 245 MET cc_start: 0.8693 (tmm) cc_final: 0.8365 (tmm) REVERT: i 270 MET cc_start: 0.8570 (mtp) cc_final: 0.7999 (mtp) REVERT: j 68 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: l 401 MET cc_start: 0.7931 (mmm) cc_final: 0.7639 (mmm) REVERT: n 30 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6580 (mmm160) REVERT: n 46 LYS cc_start: 0.7813 (tttp) cc_final: 0.7537 (tptm) REVERT: p 55 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.6640 (tptp) REVERT: p 106 ASP cc_start: 0.8652 (m-30) cc_final: 0.8124 (m-30) REVERT: r 204 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8678 (mmt) REVERT: u 17 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: u 64 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8633 (m110) REVERT: v 88 ASP cc_start: 0.8388 (m-30) cc_final: 0.8158 (m-30) outliers start: 129 outliers final: 74 residues processed: 1120 average time/residue: 1.7246 time to fit residues: 2452.0641 Evaluate side-chains 1130 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1037 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 365 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 204 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 254 GLU 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: 0.7980 chunk 150 optimal weight: 5.9990 chunk 493 optimal weight: 6.9990 chunk 528 optimal weight: 0.0770 chunk 383 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 609 optimal weight: 10.0000 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 76 ASN H 37 GLN I 13 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 l 320 ASN p 13 GLN p 124 GLN w 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 69977 Z= 0.213 Angle : 0.560 16.098 94570 Z= 0.286 Chirality : 0.042 0.236 10194 Planarity : 0.005 0.065 11771 Dihedral : 13.535 173.933 10950 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 1.76 % Allowed : 12.25 % Favored : 85.99 % 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: 1.10 (0.09), residues: 8173 helix: 1.57 (0.08), residues: 4328 sheet: 0.43 (0.26), residues: 397 loop : -0.25 (0.11), residues: 3448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS J 37 PHE 0.030 0.002 PHE i 292 TYR 0.023 0.002 TYR b 88 ARG 0.014 0.000 ARG p 65 *********************** 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 1175 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1049 time to evaluate : 5.987 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 REVERT: A 224 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.7952 (mtm180) REVERT: G 103 HIS cc_start: 0.6465 (OUTLIER) cc_final: 0.6202 (t70) REVERT: G 105 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6668 (mmt) REVERT: I 11 LEU cc_start: 0.7121 (tp) cc_final: 0.6866 (tp) REVERT: L 148 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: L 154 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8088 (ptpt) REVERT: M 666 GLN cc_start: 0.6963 (tp40) cc_final: 0.6218 (tp-100) REVERT: N 67 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7662 (tm-30) REVERT: Q 57 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6198 (pm20) REVERT: Q 99 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8159 (mtm) REVERT: Q 194 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8182 (mt) REVERT: Q 258 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8825 (tt) REVERT: S 28 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8377 (mtpt) REVERT: T 47 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6825 (p0) REVERT: T 78 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: U 41 TYR cc_start: 0.8610 (m-80) cc_final: 0.8329 (m-10) REVERT: X 82 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7885 (mtt180) REVERT: X 142 GLN cc_start: 0.8535 (tp40) cc_final: 0.8208 (tp40) REVERT: Y 41 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: Z 49 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: a 97 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: a 160 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8795 (mtt) REVERT: b 85 TYR cc_start: 0.9210 (t80) cc_final: 0.8709 (t80) REVERT: c 150 TYR cc_start: 0.7571 (m-10) cc_final: 0.7189 (m-80) REVERT: c 160 GLN cc_start: 0.8361 (mt0) cc_final: 0.8003 (mt0) REVERT: c 165 ASP cc_start: 0.7635 (t70) cc_final: 0.7091 (t70) REVERT: f 60 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8426 (mtpm) REVERT: f 68 GLU cc_start: 0.7981 (tp30) cc_final: 0.7664 (tp30) REVERT: g 47 ASP cc_start: 0.8728 (t0) cc_final: 0.8394 (t0) REVERT: h 73 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7808 (mmm) REVERT: h 85 LYS cc_start: 0.7732 (tttt) cc_final: 0.7346 (tttp) REVERT: i 245 MET cc_start: 0.8662 (tmm) cc_final: 0.8283 (tmm) REVERT: i 270 MET cc_start: 0.8554 (mtp) cc_final: 0.7990 (mtp) REVERT: j 68 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: n 30 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6571 (mmm160) REVERT: n 46 LYS cc_start: 0.7814 (tttp) cc_final: 0.7579 (tptm) REVERT: p 55 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.6698 (tptp) REVERT: p 65 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7307 (mtm110) REVERT: p 106 ASP cc_start: 0.8647 (m-30) cc_final: 0.8119 (m-30) REVERT: r 204 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8648 (mmt) REVERT: u 17 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: u 64 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8631 (m110) REVERT: v 88 ASP cc_start: 0.8382 (m-30) cc_final: 0.8132 (m-30) outliers start: 126 outliers final: 81 residues processed: 1115 average time/residue: 1.7291 time to fit residues: 2445.1126 Evaluate side-chains 1139 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1035 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 365 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 534 VAL Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 82 ARG Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 109 LEU Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 493 VAL Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 204 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 254 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.9990 chunk 743 optimal weight: 0.8980 chunk 678 optimal weight: 3.9990 chunk 723 optimal weight: 0.6980 chunk 435 optimal weight: 7.9990 chunk 314 optimal weight: 1.9990 chunk 567 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 653 optimal weight: 6.9990 chunk 683 optimal weight: 3.9990 chunk 720 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 F 76 ASN H 37 GLN ** 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 34 ASN l 320 ASN p 13 GLN p 124 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 69977 Z= 0.196 Angle : 0.551 12.410 94570 Z= 0.281 Chirality : 0.042 0.237 10194 Planarity : 0.005 0.065 11771 Dihedral : 13.282 174.118 10950 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 1.79 % Allowed : 12.20 % Favored : 86.01 % 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: 1.15 (0.09), residues: 8173 helix: 1.61 (0.08), residues: 4331 sheet: 0.46 (0.26), residues: 397 loop : -0.24 (0.11), residues: 3445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS p 51 PHE 0.030 0.001 PHE i 292 TYR 0.022 0.001 TYR b 88 ARG 0.012 0.000 ARG p 65 *********************** 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 1175 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1047 time to evaluate : 5.937 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 REVERT: A 224 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7944 (mtm180) REVERT: G 103 HIS cc_start: 0.6442 (OUTLIER) cc_final: 0.6175 (t70) REVERT: G 105 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6656 (mmt) REVERT: I 11 LEU cc_start: 0.7117 (tp) cc_final: 0.6858 (tp) REVERT: L 148 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: L 154 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8085 (ptpt) REVERT: N 67 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7635 (tm-30) REVERT: Q 57 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6201 (pm20) REVERT: Q 99 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8155 (mtm) REVERT: Q 194 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8200 (mt) REVERT: Q 258 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8842 (tt) REVERT: T 47 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6862 (p0) REVERT: T 78 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: U 41 TYR cc_start: 0.8604 (m-80) cc_final: 0.8329 (m-10) REVERT: U 47 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.8012 (ttp-110) REVERT: X 82 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7875 (mtt180) REVERT: X 142 GLN cc_start: 0.8531 (tp40) cc_final: 0.8197 (tp40) REVERT: Y 41 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7257 (mm-30) REVERT: Z 49 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: a 97 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6921 (pt0) REVERT: a 153 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: a 160 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8797 (mtt) REVERT: b 85 TYR cc_start: 0.9201 (t80) cc_final: 0.8703 (t80) REVERT: c 150 TYR cc_start: 0.7549 (m-10) cc_final: 0.7238 (m-80) REVERT: c 160 GLN cc_start: 0.8358 (mt0) cc_final: 0.7821 (mt0) REVERT: c 165 ASP cc_start: 0.7679 (t70) cc_final: 0.7124 (t70) REVERT: f 68 GLU cc_start: 0.7979 (tp30) cc_final: 0.7667 (tp30) REVERT: g 47 ASP cc_start: 0.8732 (t0) cc_final: 0.8319 (t70) REVERT: h 39 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8367 (mm-30) REVERT: h 73 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7821 (mmm) REVERT: h 85 LYS cc_start: 0.7747 (tttt) cc_final: 0.7360 (tttp) REVERT: i 245 MET cc_start: 0.8638 (tmm) cc_final: 0.8247 (tmm) REVERT: i 270 MET cc_start: 0.8541 (mtp) cc_final: 0.8111 (mtp) REVERT: j 1 MET cc_start: 0.7434 (tpp) cc_final: 0.7137 (tpt) REVERT: j 68 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: k 6 MET cc_start: 0.7953 (mtt) cc_final: 0.7690 (mtp) REVERT: l 401 MET cc_start: 0.7967 (mmm) cc_final: 0.7708 (mmm) REVERT: n 30 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6923 (mmt90) REVERT: n 46 LYS cc_start: 0.7822 (tttp) cc_final: 0.7554 (tptm) REVERT: p 55 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.6693 (tptp) REVERT: p 65 ARG cc_start: 0.7720 (mtp-110) cc_final: 0.7149 (mtm180) REVERT: p 106 ASP cc_start: 0.8642 (m-30) cc_final: 0.8114 (m-30) REVERT: r 204 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8646 (mmt) REVERT: u 17 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: u 64 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8608 (m110) REVERT: v 88 ASP cc_start: 0.8367 (m-30) cc_final: 0.8135 (m-30) REVERT: w 272 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7403 (m-30) outliers start: 128 outliers final: 82 residues processed: 1117 average time/residue: 1.7114 time to fit residues: 2428.9073 Evaluate side-chains 1144 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1037 time to evaluate : 5.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 365 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 82 ARG Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 153 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 85 MET Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 204 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 272 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 474 optimal weight: 3.9990 chunk 764 optimal weight: 5.9990 chunk 466 optimal weight: 4.9990 chunk 362 optimal weight: 7.9990 chunk 531 optimal weight: 1.9990 chunk 801 optimal weight: 0.3980 chunk 738 optimal weight: 0.7980 chunk 638 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 493 optimal weight: 5.9990 chunk 391 optimal weight: 0.4980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN J 323 HIS 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 d 124 ASN k 57 ASN l 320 ASN p 124 GLN r 138 ASN r 139 GLN w 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 0.044 69977 Z= 0.185 Angle : 0.546 12.044 94570 Z= 0.278 Chirality : 0.041 0.235 10194 Planarity : 0.005 0.065 11771 Dihedral : 13.045 174.343 10950 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 1.57 % Allowed : 12.52 % Favored : 85.92 % 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: 1.19 (0.09), residues: 8173 helix: 1.64 (0.08), residues: 4333 sheet: 0.52 (0.26), residues: 395 loop : -0.22 (0.11), residues: 3445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.007 0.001 HIS p 51 PHE 0.031 0.001 PHE i 292 TYR 0.020 0.001 TYR b 88 ARG 0.012 0.000 ARG p 65 ********************** 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 1173 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1061 time to evaluate : 5.871 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7977 (mtm180) REVERT: G 103 HIS cc_start: 0.6465 (OUTLIER) cc_final: 0.6205 (t70) REVERT: G 105 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6644 (mmt) REVERT: I 11 LEU cc_start: 0.7109 (tp) cc_final: 0.6861 (tp) REVERT: L 148 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: L 154 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8104 (ptpt) REVERT: M 670 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6393 (mt-10) REVERT: N 67 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7911 (tm-30) REVERT: Q 99 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8160 (mtm) REVERT: Q 194 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8272 (mp) REVERT: Q 258 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8839 (tt) REVERT: T 47 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6902 (p0) REVERT: T 78 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: U 41 TYR cc_start: 0.8600 (m-80) cc_final: 0.8332 (m-10) REVERT: U 47 ARG cc_start: 0.8435 (mtt-85) cc_final: 0.8030 (ttp-110) REVERT: X 82 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7899 (mtt180) REVERT: X 142 GLN cc_start: 0.8529 (tp40) cc_final: 0.8284 (tp40) REVERT: Y 41 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: Z 49 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: a 97 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6942 (pt0) REVERT: a 153 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: a 160 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8797 (mtt) REVERT: b 85 TYR cc_start: 0.9193 (t80) cc_final: 0.8720 (t80) REVERT: c 150 TYR cc_start: 0.7534 (m-10) cc_final: 0.7214 (m-80) REVERT: c 160 GLN cc_start: 0.8373 (mt0) cc_final: 0.7823 (mt0) REVERT: c 165 ASP cc_start: 0.7705 (t70) cc_final: 0.7169 (t70) REVERT: d 145 ASP cc_start: 0.8367 (m-30) cc_final: 0.8156 (m-30) REVERT: f 68 GLU cc_start: 0.7978 (tp30) cc_final: 0.7665 (tp30) REVERT: g 47 ASP cc_start: 0.8713 (t0) cc_final: 0.8295 (t70) REVERT: h 39 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8353 (mm-30) REVERT: h 73 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7791 (mmm) REVERT: h 85 LYS cc_start: 0.7747 (tttt) cc_final: 0.7359 (tttp) REVERT: i 245 MET cc_start: 0.8617 (tmm) cc_final: 0.8211 (tmm) REVERT: i 270 MET cc_start: 0.8521 (mtp) cc_final: 0.8099 (mtp) REVERT: j 1 MET cc_start: 0.7371 (tpp) cc_final: 0.7077 (tpt) REVERT: j 68 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: k 6 MET cc_start: 0.7966 (mtt) cc_final: 0.7700 (mtp) REVERT: l 401 MET cc_start: 0.7912 (mmm) cc_final: 0.7676 (mmm) REVERT: l 500 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8003 (mt) REVERT: n 30 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6806 (mmm160) REVERT: n 46 LYS cc_start: 0.7812 (tttp) cc_final: 0.7547 (tptm) REVERT: p 55 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.6698 (tptp) REVERT: p 65 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.7120 (mtm180) REVERT: p 106 ASP cc_start: 0.8637 (m-30) cc_final: 0.8107 (m-30) REVERT: r 204 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8632 (mmt) REVERT: u 17 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: u 64 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8582 (m110) REVERT: v 88 ASP cc_start: 0.8356 (m-30) cc_final: 0.8147 (m-30) REVERT: w 272 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7379 (m-30) outliers start: 112 outliers final: 76 residues processed: 1122 average time/residue: 1.7399 time to fit residues: 2479.3487 Evaluate side-chains 1147 residues out of total 7205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1046 time to evaluate : 5.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 103 HIS Chi-restraints excluded: chain G residue 105 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain I residue 41 LEU Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 351 GLU Chi-restraints excluded: chain J residue 365 GLU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 154 LYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 324 SER Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 441 ARG Chi-restraints excluded: chain M residue 575 VAL Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 194 ILE Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 258 LEU Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 78 GLU Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 58 ARG Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain X residue 82 ARG Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 62 SER Chi-restraints excluded: chain Z residue 35 LYS Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 153 GLU Chi-restraints excluded: chain a residue 160 MET Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain c residue 33 THR Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 139 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 73 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 194 LEU Chi-restraints excluded: chain j residue 16 LEU Chi-restraints excluded: chain j residue 68 GLU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 70 GLU Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 424 THR Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 491 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 30 ARG Chi-restraints excluded: chain n residue 31 SER Chi-restraints excluded: chain o residue 30 ARG Chi-restraints excluded: chain o residue 31 LYS Chi-restraints excluded: chain p residue 35 ASP Chi-restraints excluded: chain p residue 55 LYS Chi-restraints excluded: chain p residue 90 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 204 MET Chi-restraints excluded: chain s residue 251 THR Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 64 ASN Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 211 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 254 GLU Chi-restraints excluded: chain w residue 272 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 507 optimal weight: 7.9990 chunk 680 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 588 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 639 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 656 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN F 76 ASN H 37 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS M 334 GLN M 598 ASN M 663 ASN ** M 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN O 246 GLN Q 46 GLN U 40 ASN V 134 GLN b 89 HIS 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 s 99 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104484 restraints weight = 78575.641| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.07 r_work: 0.2917 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1523 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= 0.314 Angle : 0.636 13.086 94570 Z= 0.323 Chirality : 0.046 0.237 10194 Planarity : 0.005 0.066 11771 Dihedral : 13.314 172.749 10950 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 1.72 % Allowed : 12.48 % Favored : 85.80 % 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: 0.94 (0.09), residues: 8173 helix: 1.42 (0.08), residues: 4324 sheet: 0.39 (0.25), residues: 397 loop : -0.30 (0.10), residues: 3452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP u 86 HIS 0.011 0.001 HIS P 196 PHE 0.030 0.002 PHE i 292 TYR 0.034 0.002 TYR b 88 ARG 0.012 0.001 ARG p 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33019.12 seconds wall clock time: 571 minutes 7.17 seconds (34267.17 seconds total)