Starting phenix.real_space_refine on Sun Mar 24 05:34:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vys_32214/03_2024/7vys_32214_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vys_32214/03_2024/7vys_32214.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vys_32214/03_2024/7vys_32214_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/7vys_32214/03_2024/7vys_32214_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vys_32214/03_2024/7vys_32214_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vys_32214/03_2024/7vys_32214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vys_32214/03_2024/7vys_32214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vys_32214/03_2024/7vys_32214_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vys_32214/03_2024/7vys_32214_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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 293 5.16 5 C 26096 2.51 5 N 6282 2.21 5 O 7406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 45": "OE1" <-> "OE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 82": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W GLU 132": "OE1" <-> "OE2" Residue "X GLU 125": "OE1" <-> "OE2" Residue "X GLU 136": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "a PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 108": "OE1" <-> "OE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 179": "OE1" <-> "OE2" Residue "d GLU 12": "OE1" <-> "OE2" Residue "d TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 53": "OE1" <-> "OE2" Residue "d GLU 78": "OE1" <-> "OE2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d GLU 130": "OE1" <-> "OE2" Residue "e GLU 57": "OE1" <-> "OE2" Residue "e GLU 62": "OE1" <-> "OE2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "g GLU 19": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "h GLU 24": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "j GLU 105": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 268": "OE1" <-> "OE2" Residue "l GLU 503": "OE1" <-> "OE2" Residue "m GLU 139": "OE1" <-> "OE2" Residue "n GLU 33": "OE1" <-> "OE2" Residue "o GLU 113": "OE1" <-> "OE2" Residue "r GLU 47": "OE1" <-> "OE2" Residue "r GLU 123": "OE1" <-> "OE2" Residue "r GLU 141": "OE1" <-> "OE2" Residue "r GLU 378": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s GLU 143": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 17": "OE1" <-> "OE2" Residue "u GLU 80": "OE1" <-> "OE2" Residue "u GLU 84": "OE1" <-> "OE2" Residue "u GLU 149": "OE1" <-> "OE2" Residue "u GLU 153": "OE1" <-> "OE2" Residue "v GLU 16": "OE1" <-> "OE2" Residue "v GLU 36": "OE1" <-> "OE2" Residue "v GLU 83": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v GLU 103": "OE1" <-> "OE2" Residue "w GLU 47": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w GLU 79": "OE1" <-> "OE2" Residue "w GLU 115": "OE1" <-> "OE2" Residue "w GLU 254": "OE1" <-> "OE2" Residue "w GLU 271": "OE1" <-> "OE2" Residue "w GLU 303": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40113 Number of models: 1 Model: "" Number of chains: 64 Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 7, 'TRANS': 36} 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: "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: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 949 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "X" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1312 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 135} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4816 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 28, 'TRANS': 577} Chain: "m" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1292 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 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: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3619 Classifications: {'peptide': 458} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 437} 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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1022 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 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: "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: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "g" 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: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 147 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 196 Unusual residues: {'PEE': 2, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 94 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "l" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 336 Unusual residues: {'CDL': 2, 'PEE': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "r" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 115 Unusual residues: {'PEE': 1, 'PLX': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "s" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 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: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "j" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "k" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "l" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "m" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "s" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "u" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.56 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.56 Time building chain proxies: 20.87, per 1000 atoms: 0.52 Number of scatterers: 40113 At special positions: 0 Unit cell: (182.8, 193.779, 136.689, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 293 16.00 P 36 15.00 O 7406 8.00 N 6282 7.00 C 26096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.69 Conformation dependent library (CDL) restraints added in 6.6 seconds 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 203 helices and 3 sheets defined 63.0% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.048A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.626A 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 '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 'U' and resid 4 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 81 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 33 through 99 Proline residue: W 73 - end of helix removed outlier: 3.984A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 138 Processing helix chain 'X' and resid 76 through 89 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' 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: 3.763A 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: 3.791A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.674A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.182A 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 86 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 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 26 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 45 through 54 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' 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: 4.853A 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: 3.732A pdb=" N GLY d 118 " --> pdb=" O GLN d 114 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N SER d 120 " --> pdb=" O ARG d 116 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR d 121 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ARG d 122 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 6.550A 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 94 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 115 through 132 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: 3.846A 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: 3.935A 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 89 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: 3.577A 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: 4.054A pdb=" N GLU i 117 " --> pdb=" O PHE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.949A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.856A 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: 3.984A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 235 removed outlier: 3.728A pdb=" N HIS i 232 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR i 233 " --> pdb=" O SER i 229 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP i 234 " --> pdb=" O LEU i 230 " (cutoff:3.500A) removed outlier: 5.593A 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 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.515A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 310 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 56 through 80 removed outlier: 3.916A pdb=" N LEU j 67 " --> pdb=" O LEU j 63 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU j 68 " --> pdb=" O LEU j 64 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Proline residue: j 74 - end of helix removed outlier: 5.609A pdb=" N TRP j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.319A 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 55 through 85 removed outlier: 3.795A 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 4 through 23 removed outlier: 3.667A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix removed outlier: 4.962A pdb=" N ASN l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.333A 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: 3.829A 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: 3.991A 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 223 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: 3.517A pdb=" N SER l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.181A 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: 4.148A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.702A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.776A 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: 4.116A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 4.006A 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: 4.952A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.946A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 471 removed outlier: 5.927A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.454A 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: 4.057A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.481A 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: 3.985A 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 600 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 109 Processing helix chain 'm' and resid 138 through 147 removed outlier: 4.145A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR m 147 " --> pdb=" O ILE m 143 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 173 Processing helix chain 'n' and resid 4 through 14 removed outlier: 6.441A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 34 removed outlier: 3.601A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 18 No H-bonds generated for 'chain 'o' and resid 16 through 18' Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.747A 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 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 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: 4.439A 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 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 143 removed outlier: 4.918A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 5.046A 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 Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.296A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 80 Proline residue: r 74 - end of helix Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.612A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.728A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.430A 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: 3.635A pdb=" N LEU r 143 " --> pdb=" O THR r 140 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE r 151 " --> pdb=" O TYR r 148 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR r 152 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA r 155 " --> pdb=" O TYR r 152 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU r 158 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 159 - end of helix removed outlier: 4.202A 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: 4.721A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 222 removed outlier: 4.026A 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 237 through 249 removed outlier: 4.774A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) Processing helix chain 'r' and resid 254 through 257 No H-bonds generated for 'chain 'r' and resid 254 through 257' Processing helix chain 'r' and resid 259 through 277 removed outlier: 3.699A pdb=" N LEU r 277 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.674A 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 414 removed outlier: 3.678A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET r 396 " --> pdb=" O ILE r 393 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR r 403 " --> pdb=" O MET r 400 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA r 404 " --> pdb=" O MET r 401 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 454 Proline residue: r 443 - end of helix removed outlier: 3.553A pdb=" N ASN r 450 " --> pdb=" O LEU r 446 " (cutoff:3.500A) Proline residue: r 451 - end of helix removed outlier: 5.093A pdb=" N ILE r 454 " --> pdb=" O ASN r 450 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 31 Proline residue: s 12 - end of helix removed outlier: 3.781A 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: 4.233A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 123 removed outlier: 3.903A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.305A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 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: 3.619A 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 11 through 13 No H-bonds generated for 'chain 'u' and resid 11 through 13' Processing helix chain 'u' and resid 22 through 27 Processing helix chain 'u' and resid 29 through 35 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 91 removed outlier: 3.895A pdb=" N ALA u 79 " --> pdb=" O LYS u 75 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLU u 80 " --> pdb=" O ARG u 76 " (cutoff:3.500A) Proline residue: u 81 - end of helix 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 82 through 123 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 95 through 97 No H-bonds generated for 'chain 'w' and resid 95 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: 3.949A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.314A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.705A 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 231 through 252 removed outlier: 5.354A pdb=" N LEU w 246 " --> pdb=" O LYS w 242 " (cutoff:3.500A) Proline residue: w 247 - end of helix removed outlier: 3.808A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) removed outlier: 4.071A 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 275 removed outlier: 3.893A pdb=" N TYR w 275 " --> pdb=" O GLU w 271 " (cutoff:3.500A) 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: 5.332A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 333 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 'l' and resid 62 through 67 removed outlier: 6.610A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.566A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'w' and resid 84 through 86 2016 hydrogen bonds defined for protein. 5703 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: 12.51 Time building geometry restraints manager: 16.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5981 1.31 - 1.44: 11013 1.44 - 1.58: 23057 1.58 - 1.71: 118 1.71 - 1.84: 529 Bond restraints: 40698 Sorted by residual: bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C18 UQ s 402 " pdb=" C19 UQ s 402 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C13 UQ s 402 " pdb=" C14 UQ s 402 " ideal model delta sigma weight residual 1.335 1.547 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C23 UQ s 402 " pdb=" C24 UQ s 402 " ideal model delta sigma weight residual 1.335 1.543 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C8 UQ s 402 " pdb=" C9 UQ s 402 " ideal model delta sigma weight residual 1.334 1.542 -0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 40693 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.85: 1183 105.85 - 112.98: 22235 112.98 - 120.10: 14668 120.10 - 127.23: 16238 127.23 - 134.35: 581 Bond angle restraints: 54905 Sorted by residual: angle pdb=" C PRO h 94 " pdb=" N PRO h 95 " pdb=" CA PRO h 95 " ideal model delta sigma weight residual 119.66 130.06 -10.40 7.20e-01 1.93e+00 2.09e+02 angle pdb=" N TYR h 92 " pdb=" CA TYR h 92 " pdb=" C TYR h 92 " ideal model delta sigma weight residual 111.28 119.37 -8.09 1.09e+00 8.42e-01 5.51e+01 angle pdb=" C11 CDL l 702 " pdb=" CA5 CDL l 702 " pdb=" OA6 CDL l 702 " ideal model delta sigma weight residual 111.33 120.62 -9.29 1.32e+00 5.72e-01 4.94e+01 angle pdb=" C51 CDL a 201 " pdb=" CB5 CDL a 201 " pdb=" OB6 CDL a 201 " ideal model delta sigma weight residual 111.33 120.55 -9.22 1.32e+00 5.72e-01 4.87e+01 angle pdb=" C11 CDL l 703 " pdb=" CA5 CDL l 703 " pdb=" OA6 CDL l 703 " ideal model delta sigma weight residual 111.33 120.42 -9.09 1.32e+00 5.72e-01 4.73e+01 ... (remaining 54900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 23430 35.72 - 71.45: 1232 71.45 - 107.17: 85 107.17 - 142.89: 12 142.89 - 178.61: 14 Dihedral angle restraints: 24773 sinusoidal: 10910 harmonic: 13863 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual -60.00 92.85 -152.84 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" CA ARG c 114 " pdb=" C ARG c 114 " pdb=" N ASN c 115 " pdb=" CA ASN c 115 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA MET b 120 " pdb=" C MET b 120 " pdb=" N LYS b 121 " pdb=" CA LYS b 121 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 24770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5324 0.068 - 0.137: 584 0.137 - 0.205: 20 0.205 - 0.274: 3 0.274 - 0.342: 1 Chirality restraints: 5932 Sorted by residual: chirality pdb=" CA TYR h 92 " pdb=" N TYR h 92 " pdb=" C TYR h 92 " pdb=" CB TYR h 92 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA4 CDL k 101 " pdb=" CA3 CDL k 101 " pdb=" CA6 CDL k 101 " pdb=" OA6 CDL k 101 " both_signs ideal model delta sigma weight residual False -2.57 -2.36 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C2 PEE W 201 " pdb=" C1 PEE W 201 " pdb=" C3 PEE W 201 " pdb=" O2 PEE W 201 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 5929 not shown) Planarity restraints: 6678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.444 2.00e-02 2.50e+03 3.90e-01 1.90e+03 pdb=" C18 UQ s 402 " -0.469 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.408 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.012 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.421 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ s 402 " -0.075 2.00e-02 2.50e+03 2.81e-01 9.89e+02 pdb=" C11 UQ s 402 " 0.082 2.00e-02 2.50e+03 pdb=" C7 UQ s 402 " -0.271 2.00e-02 2.50e+03 pdb=" C8 UQ s 402 " 0.503 2.00e-02 2.50e+03 pdb=" C9 UQ s 402 " -0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ s 402 " -0.183 2.00e-02 2.50e+03 2.17e-01 5.88e+02 pdb=" C13 UQ s 402 " 0.120 2.00e-02 2.50e+03 pdb=" C14 UQ s 402 " 0.352 2.00e-02 2.50e+03 pdb=" C15 UQ s 402 " -0.041 2.00e-02 2.50e+03 pdb=" C16 UQ s 402 " -0.249 2.00e-02 2.50e+03 ... (remaining 6675 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 6306 2.76 - 3.47: 55872 3.47 - 4.19: 102229 4.19 - 4.90: 178405 Nonbonded interactions: 342813 Sorted by model distance: nonbonded pdb=" C LEU r 458 " pdb=" N TYR r 503 " model vdw 1.328 3.350 nonbonded pdb=" O ASP w 285 " pdb=" OD1 ASP w 285 " model vdw 2.160 3.040 nonbonded pdb=" N GLU v 38 " pdb=" OE1 GLU v 38 " model vdw 2.189 2.520 nonbonded pdb=" O HOH i 552 " pdb=" O HOH i 575 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR w 118 " pdb=" O2' ADP w 401 " model vdw 2.197 2.440 ... (remaining 342808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.56 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: 6.080 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: 24.180 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 98.540 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.150 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:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 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 : 0.008 0.226 40698 Z= 0.492 Angle : 0.851 17.458 54905 Z= 0.431 Chirality : 0.042 0.342 5932 Planarity : 0.009 0.390 6678 Dihedral : 19.884 178.615 15793 Min Nonbonded Distance : 1.328 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 0.97 % Allowed : 16.95 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.12), residues: 4666 helix: 2.07 (0.10), residues: 2940 sheet: -0.54 (0.94), residues: 23 loop : -0.48 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP w 353 HIS 0.005 0.001 HIS r 30 PHE 0.032 0.002 PHE i 292 TYR 0.024 0.001 TYR d 32 ARG 0.009 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 696 time to evaluate : 4.698 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: X 152 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8465 (mptm) REVERT: d 78 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: d 127 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7973 (tttp) REVERT: f 67 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8431 (mp) REVERT: h 101 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7392 (mttm) REVERT: m 135 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: v 103 GLU cc_start: 0.7725 (tp30) cc_final: 0.7512 (tp30) outliers start: 40 outliers final: 30 residues processed: 727 average time/residue: 1.7012 time to fit residues: 1465.6740 Evaluate side-chains 727 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 692 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 77 SER Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain X residue 152 LYS Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain d residue 136 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain w residue 152 SER Chi-restraints excluded: chain w residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 8.9990 chunk 347 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 234 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 358 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 415 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 27 HIS ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN h 21 GLN l 579 ASN o 79 ASN p 66 GLN r 83 HIS r 139 GLN s 287 HIS u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 47 ASN v 76 ASN w 323 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40698 Z= 0.219 Angle : 0.580 12.170 54905 Z= 0.294 Chirality : 0.042 0.204 5932 Planarity : 0.005 0.053 6678 Dihedral : 17.808 176.671 6624 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 2.87 % Allowed : 14.79 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.12), residues: 4666 helix: 2.03 (0.09), residues: 2952 sheet: -0.44 (0.96), residues: 23 loop : -0.49 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP w 353 HIS 0.008 0.001 HIS h 98 PHE 0.031 0.002 PHE i 292 TYR 0.023 0.002 TYR l 587 ARG 0.008 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 710 time to evaluate : 3.498 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 79 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: W 51 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8466 (ttm) REVERT: W 85 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: W 121 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.6955 (ttt) REVERT: a 72 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8130 (ttm170) REVERT: b 17 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: c 36 MET cc_start: 0.7400 (mtm) cc_final: 0.6753 (mmp) REVERT: d 85 MET cc_start: 0.9018 (mtp) cc_final: 0.8710 (mtp) REVERT: e 55 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6677 (tt) REVERT: e 78 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8310 (ptpt) REVERT: f 67 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8424 (mp) REVERT: h 53 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7566 (tm-30) REVERT: l 383 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7006 (tmt) REVERT: r 114 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: r 144 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8384 (t0) REVERT: r 401 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8585 (tmm) REVERT: u 17 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: w 293 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7595 (ttp-110) outliers start: 118 outliers final: 44 residues processed: 773 average time/residue: 1.7301 time to fit residues: 1592.0456 Evaluate side-chains 749 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 690 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 69 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 272 ASP Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 346 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 416 optimal weight: 0.7980 chunk 450 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 413 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 334 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN h 21 GLN p 66 GLN r 139 GLN r 192 ASN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 40698 Z= 0.283 Angle : 0.622 11.625 54905 Z= 0.318 Chirality : 0.044 0.213 5932 Planarity : 0.005 0.049 6678 Dihedral : 17.020 177.575 6576 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 3.08 % Allowed : 15.06 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.12), residues: 4666 helix: 1.88 (0.09), residues: 2957 sheet: -0.40 (0.96), residues: 23 loop : -0.56 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP l 144 HIS 0.006 0.001 HIS r 30 PHE 0.030 0.002 PHE i 292 TYR 0.027 0.002 TYR l 587 ARG 0.008 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 697 time to evaluate : 4.558 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 62 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7811 (mtpp) REVERT: U 10 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7546 (tppp) REVERT: U 79 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: W 51 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8402 (ttm) REVERT: W 85 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: W 121 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.6849 (ttt) REVERT: a 72 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8161 (ttm170) REVERT: b 17 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: c 36 MET cc_start: 0.7773 (mtm) cc_final: 0.7128 (mmp) REVERT: e 55 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6764 (tt) REVERT: e 69 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7904 (mmtp) REVERT: e 78 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8325 (ptpt) REVERT: f 67 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8442 (mp) REVERT: h 53 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7529 (tm-30) REVERT: l 70 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8688 (m) REVERT: l 383 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7196 (tmt) REVERT: l 496 MET cc_start: 0.7763 (mmt) cc_final: 0.7557 (mmt) REVERT: m 135 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: n 15 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8701 (pp) REVERT: r 114 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: r 144 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8421 (t0) REVERT: r 401 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8607 (tmm) REVERT: s 24 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: u 17 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: v 15 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7389 (mtmt) REVERT: v 103 GLU cc_start: 0.7785 (tp30) cc_final: 0.7542 (tp30) REVERT: w 293 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7614 (ttp-110) outliers start: 127 outliers final: 52 residues processed: 766 average time/residue: 1.7537 time to fit residues: 1596.9669 Evaluate side-chains 761 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 687 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 62 LYS Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 272 ASP Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 411 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 198 optimal weight: 4.9990 chunk 279 optimal weight: 9.9990 chunk 418 optimal weight: 4.9990 chunk 442 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 396 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN e 86 ASN e 132 ASN i 319 HIS l 579 ASN p 66 GLN r 139 GLN r 192 ASN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40698 Z= 0.220 Angle : 0.574 10.554 54905 Z= 0.293 Chirality : 0.042 0.206 5932 Planarity : 0.005 0.049 6678 Dihedral : 16.463 169.679 6574 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 3.01 % Allowed : 15.61 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.12), residues: 4666 helix: 1.98 (0.09), residues: 2952 sheet: -0.32 (0.97), residues: 23 loop : -0.48 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP w 353 HIS 0.005 0.001 HIS i 319 PHE 0.032 0.002 PHE i 292 TYR 0.023 0.002 TYR l 587 ARG 0.007 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 685 time to evaluate : 4.233 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 32 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8494 (mp) REVERT: U 79 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: W 51 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8352 (ttm) REVERT: W 85 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: W 121 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.6836 (ttt) REVERT: a 72 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8154 (ttm170) REVERT: b 17 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: c 36 MET cc_start: 0.7849 (mtm) cc_final: 0.7208 (mmp) REVERT: e 55 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6655 (tt) REVERT: e 69 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7787 (mmtp) REVERT: e 78 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8326 (ptpt) REVERT: f 67 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8402 (mp) REVERT: h 53 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7498 (tm-30) REVERT: l 70 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8667 (m) REVERT: l 286 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8749 (tp) REVERT: l 383 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7120 (tmt) REVERT: n 15 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8675 (pp) REVERT: p 135 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7273 (ttp-110) REVERT: r 114 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: r 144 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8392 (t0) REVERT: r 401 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8564 (tmm) REVERT: s 24 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: u 17 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: v 16 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: v 103 GLU cc_start: 0.7801 (tp30) cc_final: 0.7567 (tp30) REVERT: w 293 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7612 (ttp-110) outliers start: 124 outliers final: 50 residues processed: 756 average time/residue: 1.7132 time to fit residues: 1541.3383 Evaluate side-chains 747 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 674 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain e residue 55 LEU Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 52 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 368 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 306 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 397 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN e 132 ASN i 171 ASN i 319 HIS p 66 GLN r 139 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40698 Z= 0.180 Angle : 0.540 10.681 54905 Z= 0.275 Chirality : 0.040 0.198 5932 Planarity : 0.005 0.048 6678 Dihedral : 15.822 163.256 6574 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.44 % Rotamer: Outliers : 2.72 % Allowed : 16.12 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.12), residues: 4666 helix: 2.08 (0.10), residues: 2951 sheet: -0.18 (1.00), residues: 23 loop : -0.41 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 86 HIS 0.004 0.001 HIS r 30 PHE 0.032 0.001 PHE i 292 TYR 0.021 0.001 TYR l 587 ARG 0.009 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 702 time to evaluate : 4.826 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 10 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7579 (tppp) REVERT: U 32 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8448 (mp) REVERT: U 79 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: W 51 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8441 (ttm) REVERT: W 85 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: b 17 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: c 36 MET cc_start: 0.7862 (mtm) cc_final: 0.7238 (mmp) REVERT: d 85 MET cc_start: 0.9016 (mtp) cc_final: 0.8692 (mtp) REVERT: e 69 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7760 (mmtp) REVERT: e 78 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8320 (ptpt) REVERT: f 67 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8362 (mp) REVERT: h 24 GLU cc_start: 0.7561 (tp30) cc_final: 0.7342 (tp30) REVERT: h 53 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7487 (tm-30) REVERT: i 263 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8058 (mmtm) REVERT: l 383 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7098 (tmt) REVERT: n 15 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8650 (pp) REVERT: r 114 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: r 144 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8377 (t0) REVERT: u 17 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: v 15 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7579 (mtpt) REVERT: v 16 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: v 103 GLU cc_start: 0.7799 (tp30) cc_final: 0.7572 (tp30) REVERT: w 45 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6710 (pp) REVERT: w 293 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7602 (ttp-110) outliers start: 112 outliers final: 49 residues processed: 767 average time/residue: 1.6858 time to fit residues: 1541.6330 Evaluate side-chains 748 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 681 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 137 LYS Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 426 ILE Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 52 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 148 optimal weight: 9.9990 chunk 398 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 443 optimal weight: 8.9990 chunk 367 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN e 132 ASN i 147 GLN ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS p 66 GLN r 192 ASN u 64 ASN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 40698 Z= 0.332 Angle : 0.653 10.892 54905 Z= 0.334 Chirality : 0.046 0.218 5932 Planarity : 0.006 0.056 6678 Dihedral : 16.064 164.982 6570 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 3.25 % Allowed : 15.76 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.12), residues: 4666 helix: 1.78 (0.09), residues: 2968 sheet: -0.22 (0.99), residues: 23 loop : -0.55 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP l 144 HIS 0.007 0.001 HIS i 319 PHE 0.031 0.002 PHE r 122 TYR 0.029 0.002 TYR l 587 ARG 0.010 0.001 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 676 time to evaluate : 4.916 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 74 ASP cc_start: 0.5197 (OUTLIER) cc_final: 0.4935 (p0) REVERT: U 10 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7801 (tppp) REVERT: U 79 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: W 51 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8407 (ttm) REVERT: W 85 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: W 108 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: W 121 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.6864 (ttt) REVERT: a 72 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8170 (ttm170) REVERT: b 17 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: c 36 MET cc_start: 0.7939 (mtm) cc_final: 0.7340 (mmp) REVERT: d 127 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8006 (tttp) REVERT: e 69 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7953 (mmtp) REVERT: e 78 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8327 (ptpt) REVERT: f 67 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8441 (mp) REVERT: h 24 GLU cc_start: 0.7645 (tp30) cc_final: 0.7415 (tp30) REVERT: h 53 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7503 (tm-30) REVERT: i 88 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6416 (ttmp) REVERT: j 69 ILE cc_start: 0.8570 (mm) cc_final: 0.8321 (mt) REVERT: l 70 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8674 (m) REVERT: l 286 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8743 (tp) REVERT: l 383 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7188 (tmt) REVERT: n 15 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8722 (pp) REVERT: p 135 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7361 (ttp-110) REVERT: r 114 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: r 144 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8430 (t0) REVERT: r 418 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8746 (tttt) REVERT: s 202 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: u 17 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: v 16 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: v 103 GLU cc_start: 0.7828 (tp30) cc_final: 0.7612 (tp30) REVERT: w 45 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6868 (pp) REVERT: w 293 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7617 (ttp-110) outliers start: 134 outliers final: 64 residues processed: 757 average time/residue: 1.7639 time to fit residues: 1587.8367 Evaluate side-chains 758 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 667 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 94 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 418 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 254 LEU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 52 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 272 ASP Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 427 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 323 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 441 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 269 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN e 132 ASN ** i 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS p 66 GLN r 139 GLN u 64 ASN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 40698 Z= 0.291 Angle : 0.628 11.010 54905 Z= 0.322 Chirality : 0.045 0.216 5932 Planarity : 0.005 0.056 6678 Dihedral : 15.956 166.649 6570 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 3.04 % Allowed : 16.08 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.12), residues: 4666 helix: 1.81 (0.09), residues: 2950 sheet: -0.19 (0.99), residues: 23 loop : -0.54 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP l 144 HIS 0.006 0.001 HIS r 30 PHE 0.030 0.002 PHE i 292 TYR 0.026 0.002 TYR l 587 ARG 0.011 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 671 time to evaluate : 3.892 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: Q 74 ASP cc_start: 0.5168 (OUTLIER) cc_final: 0.4924 (p0) REVERT: U 10 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7765 (tppp) REVERT: U 79 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: W 51 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8396 (ttm) REVERT: W 85 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: W 108 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: W 121 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.6856 (ttt) REVERT: a 72 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8168 (ttm170) REVERT: b 17 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: c 36 MET cc_start: 0.7961 (mtm) cc_final: 0.7373 (mmp) REVERT: d 127 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7987 (tttp) REVERT: e 69 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7857 (mmtp) REVERT: e 78 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8332 (ptpt) REVERT: f 67 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8422 (mp) REVERT: h 24 GLU cc_start: 0.7632 (tp30) cc_final: 0.7397 (tp30) REVERT: h 53 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7491 (tm-30) REVERT: l 70 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8701 (m) REVERT: l 383 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7213 (tmt) REVERT: n 15 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8710 (pp) REVERT: p 135 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7334 (ttp-110) REVERT: r 114 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: r 144 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8424 (t0) REVERT: r 418 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8751 (tttt) REVERT: s 202 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: u 17 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: v 15 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7482 (mtmt) REVERT: v 16 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: v 103 GLU cc_start: 0.7823 (tp30) cc_final: 0.7611 (tp30) REVERT: w 45 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6930 (pp) REVERT: w 293 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7616 (ttp-110) outliers start: 125 outliers final: 64 residues processed: 744 average time/residue: 1.7841 time to fit residues: 1573.3124 Evaluate side-chains 752 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 663 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 74 ASP Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Z residue 79 VAL Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 215 MET Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 94 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 599 MET Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 183 SER Chi-restraints excluded: chain r residue 418 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain s residue 254 LEU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 52 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 273 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 263 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 85 optimal weight: 0.0670 chunk 280 optimal weight: 6.9990 chunk 300 optimal weight: 0.6980 chunk 218 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 346 optimal weight: 50.0000 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN e 132 ASN ** i 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 171 ASN i 319 HIS p 66 GLN r 139 GLN r 192 ASN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40698 Z= 0.193 Angle : 0.560 11.498 54905 Z= 0.286 Chirality : 0.041 0.202 5932 Planarity : 0.005 0.046 6678 Dihedral : 15.425 167.513 6570 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 2.74 % Allowed : 16.61 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.12), residues: 4666 helix: 2.00 (0.10), residues: 2949 sheet: -0.11 (1.01), residues: 23 loop : -0.46 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP l 144 HIS 0.005 0.001 HIS r 30 PHE 0.032 0.002 PHE i 292 TYR 0.021 0.001 TYR l 587 ARG 0.008 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 675 time to evaluate : 4.742 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 10 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7602 (tppp) REVERT: U 79 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: W 51 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8328 (ttm) REVERT: W 85 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: W 108 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: W 121 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.6836 (ttt) REVERT: a 72 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8130 (ttm170) REVERT: b 17 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: c 36 MET cc_start: 0.7928 (mtm) cc_final: 0.7365 (mmp) REVERT: d 85 MET cc_start: 0.9043 (mtp) cc_final: 0.8696 (mtp) REVERT: e 69 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7737 (mmtp) REVERT: e 78 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8325 (ptpt) REVERT: f 67 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8370 (mp) REVERT: h 24 GLU cc_start: 0.7561 (tp30) cc_final: 0.7318 (tp30) REVERT: h 53 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7477 (tm-30) REVERT: i 88 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6204 (ttmp) REVERT: i 263 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8122 (mmtm) REVERT: l 286 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8587 (tp) REVERT: l 383 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7116 (tmt) REVERT: n 15 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8668 (pp) REVERT: p 135 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7231 (ttp-110) REVERT: r 114 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: r 144 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8375 (t0) REVERT: r 401 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8493 (tmm) REVERT: s 202 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: u 17 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: v 16 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: v 21 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6841 (mmt90) REVERT: v 103 GLU cc_start: 0.7809 (tp30) cc_final: 0.7600 (tp30) REVERT: w 45 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6786 (pp) REVERT: w 293 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7604 (ttp-110) outliers start: 113 outliers final: 57 residues processed: 739 average time/residue: 1.7677 time to fit residues: 1556.9774 Evaluate side-chains 753 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 670 time to evaluate : 4.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 94 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 286 LEU Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain m residue 50 SER Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 52 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 401 optimal weight: 3.9990 chunk 422 optimal weight: 10.0000 chunk 385 optimal weight: 0.7980 chunk 411 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 323 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 371 optimal weight: 8.9990 chunk 389 optimal weight: 1.9990 chunk 409 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN e 132 ASN ** i 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS p 66 GLN r 192 ASN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40698 Z= 0.239 Angle : 0.597 11.855 54905 Z= 0.305 Chirality : 0.043 0.206 5932 Planarity : 0.005 0.053 6678 Dihedral : 15.312 169.802 6570 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 2.45 % Allowed : 16.95 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.12), residues: 4666 helix: 1.95 (0.09), residues: 2945 sheet: -0.09 (1.02), residues: 23 loop : -0.46 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP l 144 HIS 0.006 0.001 HIS r 30 PHE 0.031 0.002 PHE i 292 TYR 0.024 0.002 TYR l 587 ARG 0.010 0.000 ARG m 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 674 time to evaluate : 4.738 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 10 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7635 (tppp) REVERT: U 79 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: W 51 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: W 85 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: W 108 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: W 121 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.6839 (ttt) REVERT: a 72 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8153 (ttm170) REVERT: b 17 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: c 36 MET cc_start: 0.7949 (mtm) cc_final: 0.7385 (mmp) REVERT: d 15 ARG cc_start: 0.7105 (ttm110) cc_final: 0.6552 (tpp80) REVERT: d 127 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7985 (tttp) REVERT: e 69 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7856 (mmtp) REVERT: e 78 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8326 (ptpt) REVERT: f 67 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8381 (mp) REVERT: h 53 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7486 (tm-30) REVERT: i 88 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6271 (ttmp) REVERT: i 263 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8147 (mmtm) REVERT: l 70 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8688 (m) REVERT: l 383 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7233 (tmt) REVERT: n 15 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8686 (pp) REVERT: p 135 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7278 (ttp-110) REVERT: p 138 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7436 (tmmt) REVERT: r 114 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: r 144 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8404 (t0) REVERT: r 401 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8524 (tmm) REVERT: s 202 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: u 17 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: v 16 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: v 21 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6812 (mmt90) REVERT: v 103 GLU cc_start: 0.7817 (tp30) cc_final: 0.7608 (tp30) REVERT: w 45 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6822 (pp) REVERT: w 293 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7605 (ttp-110) outliers start: 101 outliers final: 60 residues processed: 729 average time/residue: 1.7758 time to fit residues: 1536.6928 Evaluate side-chains 761 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 673 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 94 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain r residue 401 MET Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 52 LYS Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 270 optimal weight: 9.9990 chunk 434 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 456 optimal weight: 6.9990 chunk 419 optimal weight: 8.9990 chunk 363 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 280 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN e 132 ASN ** i 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS n 11 HIS p 66 GLN r 139 GLN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN v 110 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 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 0.055 40698 Z= 0.254 Angle : 0.610 11.800 54905 Z= 0.311 Chirality : 0.043 0.210 5932 Planarity : 0.005 0.058 6678 Dihedral : 15.232 173.163 6570 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 2.28 % Allowed : 17.07 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.12), residues: 4666 helix: 1.91 (0.09), residues: 2944 sheet: -0.10 (1.02), residues: 23 loop : -0.47 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP l 144 HIS 0.006 0.001 HIS r 30 PHE 0.031 0.002 PHE i 292 TYR 0.025 0.002 TYR l 587 ARG 0.011 0.000 ARG m 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9332 Ramachandran restraints generated. 4666 Oldfield, 0 Emsley, 4666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 672 time to evaluate : 4.499 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. REVERT: U 10 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7626 (tppp) REVERT: U 79 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: W 51 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8361 (ttm) REVERT: W 85 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: W 98 MET cc_start: 0.7360 (mmm) cc_final: 0.6750 (mmt) REVERT: W 108 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: W 121 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.6852 (ttt) REVERT: a 72 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8159 (ttm170) REVERT: b 17 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: c 36 MET cc_start: 0.7956 (mtm) cc_final: 0.7400 (mmp) REVERT: d 15 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6539 (tpp80) REVERT: d 127 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7981 (tttp) REVERT: e 69 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7860 (mmtp) REVERT: e 78 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8316 (ptpt) REVERT: f 67 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8396 (mp) REVERT: h 53 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7488 (tm-30) REVERT: i 88 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6282 (ttmp) REVERT: i 263 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8182 (mmtm) REVERT: l 70 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8694 (m) REVERT: l 383 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7247 (tmt) REVERT: n 15 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8687 (pp) REVERT: p 135 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7303 (ttp-110) REVERT: p 138 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7444 (tmmt) REVERT: r 114 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: r 144 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8405 (t0) REVERT: s 202 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: u 17 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7257 (mm-30) REVERT: v 15 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7531 (mtmm) REVERT: v 16 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: v 21 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6817 (mmt90) REVERT: v 103 GLU cc_start: 0.7809 (tp30) cc_final: 0.7601 (tp30) REVERT: w 45 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6849 (pp) REVERT: w 271 GLU cc_start: 0.7337 (pt0) cc_final: 0.6985 (pt0) REVERT: w 293 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7611 (ttp-110) outliers start: 94 outliers final: 59 residues processed: 721 average time/residue: 1.8036 time to fit residues: 1545.1933 Evaluate side-chains 756 residues out of total 4157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 670 time to evaluate : 4.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 79 GLU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 51 MET Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 85 GLN Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 121 MET Chi-restraints excluded: chain X residue 102 SER Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain a residue 58 LYS Chi-restraints excluded: chain a residue 72 ARG Chi-restraints excluded: chain a residue 77 LEU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 127 LYS Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 78 LYS Chi-restraints excluded: chain e residue 81 ILE Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 29 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 THR Chi-restraints excluded: chain i residue 88 LYS Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 263 LYS Chi-restraints excluded: chain i residue 275 SER Chi-restraints excluded: chain i residue 308 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 26 GLN Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 94 LEU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 349 SER Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 486 MET Chi-restraints excluded: chain l residue 554 ASP Chi-restraints excluded: chain l residue 601 LEU Chi-restraints excluded: chain m residue 76 THR Chi-restraints excluded: chain m residue 167 VAL Chi-restraints excluded: chain n residue 4 VAL Chi-restraints excluded: chain n residue 8 VAL Chi-restraints excluded: chain n residue 15 ILE Chi-restraints excluded: chain o residue 9 SER Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 135 ARG Chi-restraints excluded: chain p residue 138 LYS Chi-restraints excluded: chain p residue 176 GLU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 114 GLU Chi-restraints excluded: chain r residue 144 ASN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 246 ILE Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 40 VAL Chi-restraints excluded: chain s residue 87 VAL Chi-restraints excluded: chain s residue 110 SER Chi-restraints excluded: chain s residue 167 THR Chi-restraints excluded: chain s residue 202 GLU Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 68 LEU Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain v residue 54 GLN Chi-restraints excluded: chain w residue 45 LEU Chi-restraints excluded: chain w residue 203 VAL Chi-restraints excluded: chain w residue 253 CYS Chi-restraints excluded: chain w residue 270 VAL Chi-restraints excluded: chain w residue 293 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 288 optimal weight: 7.9990 chunk 387 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 335 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.0030 chunk 363 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 373 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 49 GLN e 132 ASN ** i 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS n 11 HIS p 66 GLN r 139 GLN r 192 ASN u 65 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 GLN v 47 ASN v 76 ASN v 110 GLN ** w 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.104979 restraints weight = 41877.872| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.00 r_work: 0.2943 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40698 Z= 0.196 Angle : 0.565 11.874 54905 Z= 0.288 Chirality : 0.041 0.200 5932 Planarity : 0.005 0.052 6678 Dihedral : 14.903 175.253 6570 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 2.26 % Allowed : 17.17 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.12), residues: 4666 helix: 2.01 (0.10), residues: 2949 sheet: -0.04 (1.03), residues: 23 loop : -0.42 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP l 144 HIS 0.005 0.001 HIS r 30 PHE 0.032 0.002 PHE i 292 TYR 0.027 0.001 TYR c 150 ARG 0.010 0.000 ARG m 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22871.40 seconds wall clock time: 404 minutes 35.21 seconds (24275.21 seconds total)